error information improved

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java

@@ -61,91 +61,98 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
 
     String speciesId = getNodeAttr("species", aliasNode);
     String aliasId = getNodeAttr("id", aliasNode);
+
+    String errorPrefix = "[" + speciesId + "," + aliasId + "]\t";
     CellDesignerSpecies<?> species = elements.getElementByElementId(speciesId);
     if (species == null) {
       throw new InvalidXmlSchemaException("Unknown species for alias (speciesId: " + speciesId + ")");
     }
     if (species instanceof CellDesignerComplexSpecies) {
-      logger.warn("[" + speciesId + "," + aliasId
-          + "]\tSpecies is defined as a complex, but alias is not a complex. Changing alias to complex.");
+      logger.warn(
+          errorPrefix + "Species is defined as a complex, but alias is not a complex. Changing alias to complex.");
     }
 
     elements.addElement(species, aliasId);
-    Species result = species.createModelElement(aliasId);
-
-    String state = "usual";
-    NodeList nodes = aliasNode.getChildNodes();
-    View usualView = null;
-    View briefView = null;
-    for (int x = 0; x < nodes.getLength(); x++) {
-      Node node = nodes.item(x);
-      if (node.getNodeType() == Node.ELEMENT_NODE) {
-        if (node.getNodeName().equalsIgnoreCase("celldesigner:activity")) {
-          result.setActivity(getNodeValue(node).equalsIgnoreCase("active"));
-        } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
-          result.setX(getNodeAttr("X", node));
-          result.setY(getNodeAttr("Y", node));
-        } else if (node.getNodeName().equalsIgnoreCase("celldesigner:font")) {
-          result.setFontSize(getNodeAttr("size", node));
-        } else if (node.getNodeName().equalsIgnoreCase("celldesigner:view")) {
-          state = getNodeAttr("state", node);
-        } else if (node.getNodeName().equalsIgnoreCase("celldesigner:usualView")) {
-          usualView = getCommonParser().getView(node);
-        } else if (node.getNodeName().equalsIgnoreCase("celldesigner:briefView")) {
-          briefView = getCommonParser().getView(node);
-        } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
-          processAliasState(node, result);
-        } else if (node.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
-          // not handled
-          continue;
-        } else {
-          throw new InvalidXmlSchemaException("Unknown element of celldesigner:speciesAlias: " + node.getNodeName());
+    try {
+      Species result = species.createModelElement(aliasId);
+
+      String state = "usual";
+      NodeList nodes = aliasNode.getChildNodes();
+      View usualView = null;
+      View briefView = null;
+      for (int x = 0; x < nodes.getLength(); x++) {
+        Node node = nodes.item(x);
+        if (node.getNodeType() == Node.ELEMENT_NODE) {
+          if (node.getNodeName().equalsIgnoreCase("celldesigner:activity")) {
+            result.setActivity(getNodeValue(node).equalsIgnoreCase("active"));
+          } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
+            result.setX(getNodeAttr("X", node));
+            result.setY(getNodeAttr("Y", node));
+          } else if (node.getNodeName().equalsIgnoreCase("celldesigner:font")) {
+            result.setFontSize(getNodeAttr("size", node));
+          } else if (node.getNodeName().equalsIgnoreCase("celldesigner:view")) {
+            state = getNodeAttr("state", node);
+          } else if (node.getNodeName().equalsIgnoreCase("celldesigner:usualView")) {
+            usualView = getCommonParser().getView(node);
+          } else if (node.getNodeName().equalsIgnoreCase("celldesigner:briefView")) {
+            briefView = getCommonParser().getView(node);
+          } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
+            processAliasState(node, result);
+          } else if (node.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
+            // not handled
+            continue;
+          } else {
+            throw new InvalidXmlSchemaException(
+                errorPrefix + "Unknown element of celldesigner:speciesAlias: " + node.getNodeName());
+          }
         }
       }
-    }
 
-    View view = null;
-    if (state.equalsIgnoreCase("usual")) {
-      view = usualView;
-    } else if (state.equalsIgnoreCase("brief")) {
-      view = briefView;
-    }
+      View view = null;
+      if (state.equalsIgnoreCase("usual")) {
+        view = usualView;
+      } else if (state.equalsIgnoreCase("brief")) {
+        view = briefView;
+      }
 
-    if (view != null) {
-      // inner position defines the position in compartment
-      // result.moveBy(view.innerPosition);
-      result.setWidth(view.getBoxSize().width);
-      result.setHeight(view.getBoxSize().height);
-      result.setLineWidth(view.getSingleLine().getWidth());
-      result.setColor(view.getColor());
-    } else {
-      throw new InvalidXmlSchemaException("No view in Alias");
-    }
-    result.setState(state);
-    String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
-    if (!compartmentAliasId.isEmpty()) {
-      Compartment compartment = model.getElementByElementId(compartmentAliasId);
-      if (compartment == null) {
-        throw new InvalidXmlSchemaException("CompartmentAlias does not exist: " + compartmentAliasId);
+      if (view != null) {
+        // inner position defines the position in compartment
+        // result.moveBy(view.innerPosition);
+        result.setWidth(view.getBoxSize().width);
+        result.setHeight(view.getBoxSize().height);
+        result.setLineWidth(view.getSingleLine().getWidth());
+        result.setColor(view.getColor());
       } else {
-        result.setCompartment(compartment);
-        compartment.addElement(result);
+        throw new InvalidXmlSchemaException(errorPrefix + "No view in Alias");
       }
-    }
-    String complexAliasId = getNodeAttr("complexSpeciesAlias", aliasNode);
-    if (!complexAliasId.isEmpty()) {
-      Complex complex = model.getElementByElementId(complexAliasId);
-      if (complex == null) {
-        throw new InvalidXmlSchemaException(
-            "ComplexAlias does not exist: " + complexAliasId + ", current: " + result.getElementId());
-      } else {
-        result.setComplex(complex);
-        complex.addSpecies(result);
+      result.setState(state);
+      String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
+      if (!compartmentAliasId.isEmpty()) {
+        Compartment compartment = model.getElementByElementId(compartmentAliasId);
+        if (compartment == null) {
+          throw new InvalidXmlSchemaException(errorPrefix + "CompartmentAlias does not exist: " + compartmentAliasId);
+        } else {
+          result.setCompartment(compartment);
+          compartment.addElement(result);
+        }
+      }
+      String complexAliasId = getNodeAttr("complexSpeciesAlias", aliasNode);
+      if (!complexAliasId.isEmpty()) {
+        Complex complex = model.getElementByElementId(complexAliasId);
+        if (complex == null) {
+          throw new InvalidXmlSchemaException(
+              errorPrefix + "ComplexAlias does not exist: " + complexAliasId + ", current: " + result.getElementId());
+        } else {
+          result.setComplex(complex);
+          complex.addSpecies(result);
+        }
       }
-    }
 
-    species.updateModelElementAfterLayoutAdded(result);
-    return result;
+      species.updateModelElementAfterLayoutAdded(result);
+      return result;
+    } catch (NotImplementedException e) {
+      throw new InvalidXmlSchemaException(errorPrefix + "Problem with creating species");
+    }
   }
 
   /**