color definitions are supported

commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java

@@ -56,7 +56,7 @@ public class ColorParser {
       throw new InvalidArgumentException(
           "Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
     }
-    
+
     if (string.charAt(0) != '#') {
       string = "#" + string;
     }
@@ -86,10 +86,15 @@ public class ColorParser {
       throw new InvalidArgumentException(
           "Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
     } else {
-      return new Color(
-          Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE),
-          Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE),
-          Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH_WITHOUT_ALPHA), HEX_BASE));
+      try {
+        return new Color(
+            Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE),
+            Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE),
+            Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH_WITHOUT_ALPHA), HEX_BASE));
+      } catch (NumberFormatException e) {
+        throw new InvalidArgumentException(
+            "Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
+      }
     }
   }
 
@@ -112,12 +117,17 @@ public class ColorParser {
       throw new InvalidArgumentException(
           "Invalid color value: " + string + ". Correct format: #xxxxxxxx (where x is a hex value)");
     } else {
-      return new Color(
-          Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE),
-          Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE),
-          Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH_WITHOUT_ALPHA), HEX_BASE),
-          Integer.valueOf(string.substring(COLOR_STRING_LENGTH_WITHOUT_ALPHA, COLOR_STRING_LENGTH_WITH_ALPHA), HEX_BASE)
-          );
+      try {
+        return new Color(
+            Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE),
+            Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE),
+            Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH_WITHOUT_ALPHA), HEX_BASE),
+            Integer.valueOf(string.substring(COLOR_STRING_LENGTH_WITHOUT_ALPHA, COLOR_STRING_LENGTH_WITH_ALPHA),
+                HEX_BASE));
+      } catch (NumberFormatException e) {
+        throw new InvalidArgumentException(
+            "Invalid color value: " + string + ". Correct format: #xxxxxxxx (where x is a hex value)");
+      }
     }
   }
 

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

@@ -724,13 +724,13 @@ public class SbgnmlXmlParser {
       Style style = RenderUtil.getStyle(renderInformation, glyph);
       if (style != null) {
         try {
-          element.setFillColor(colorParser.parse(style.getG().getFill()));
+          element.setFillColor(extractColor(style.getG().getFill()));
         } catch (InvalidArgumentException e) {
           logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, element),
               "Invalid fill color: " + style.getG().getFill());
         }
         try {
-          element.setBorderColor(colorParser.parse(style.getG().getStroke()));
+          element.setBorderColor(extractColor(style.getG().getStroke()));
         } catch (InvalidArgumentException e) {
           logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, element),
               "Invalid border color: " + style.getG().getStroke());
@@ -746,6 +746,29 @@ public class SbgnmlXmlParser {
     }
   }
 
+  private Color extractColor(String fill) {
+    Color color = getRenderColor(fill);
+    if (color == null) {
+      color = colorParser.parse(fill);
+    }
+    return color;
+  }
+
+  private Color getRenderColor(String color) {
+    ColorDefinition colorDefinition = RenderUtil.getColorDefinition(renderInformation, color);
+    if (colorDefinition != null) {
+      return colorParser.parse(colorDefinition.getValue());
+    }
+    LinearGradient gradient = RenderUtil.getGradient(renderInformation, color);
+    if (gradient != null) {
+      if (gradient.getStop().size() > 0) {
+        return colorParser.parse(gradient.getStop().get(0).getStopColor());
+      }
+    }
+
+    return null;
+  }
+
   private void assignRenderInformation(PolylineData line, Arc glyph) {
     if (renderInformation != null) {
       Style style = RenderUtil.getStyle(renderInformation, glyph);
@@ -756,10 +779,9 @@ public class SbgnmlXmlParser {
   private void assignRenderInformation(PolylineData line, Style style) {
     if (style != null) {
       try {
-        Color color = colorParser.parse(style.getG().getStroke());
-        line.setColor(color);
+        line.setColor(extractColor(style.getG().getStroke()));
       } catch (InvalidArgumentException e) {
-        logger.warn("Invalid border color: " + style.getG().getStroke());
+        logger.warn("Invalid line color: " + style.getG().getStroke());
       }
       if (style.getG().getStrokeWidth() != null) {
         double lineWidth = (double) style.getG().getStrokeWidth();

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java

@@ -15,3 +15,4 @@ import org.junit.runners.Suite.SuiteClasses;
 public class AllSbgnmlTests {
 
 }
+

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java

@@ -2,6 +2,7 @@ package lcsb.mapviewer.converter.model.sbgnml;
 
 import static org.junit.Assert.*;
 
+import java.awt.Color;
 import java.awt.geom.Point2D;
 
 import org.apache.logging.log4j.LogManager;
@@ -115,6 +116,16 @@ public class SbgnmlXmlParserTest2 extends SbgnmlTestFunctions {
     assertEquals(0, protein.getModificationResidues().size());
   }
 
+  @Test
+  public void testParseColors() throws Exception {
+    Converter converter = new SbgnmlXmlConverter();
+    Model model = converter
+        .createModel(new ConverterParams()
+            .filename("testFiles/sbgnmlCellDesignerInompatible/neuronal_muscle_signalling_color.sbgn"));
+    assertFalse(model.getElementByElementId("glyph0").getFillColor().equals(Color.WHITE));
+    assertTrue(super.getWarnings().size() <= 1);
+  }
+
   @Test
   public void testProblematicProduct() throws Exception {
     Converter converter = new SbgnmlXmlConverter();