import/export of colors added

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

 package lcsb.mapviewer.converter.model.sbgnml;
 
+import java.awt.Color;
 import java.awt.geom.Point2D;
+import java.io.IOException;
 import java.util.*;
 import java.util.stream.Collectors;
 
+import javax.xml.bind.JAXBException;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.stream.XMLStreamException;
+
 import org.apache.commons.lang3.RandomStringUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
@@ -12,9 +18,12 @@ import org.sbgn.*;
 import org.sbgn.bindings.*;
 import org.sbgn.bindings.Arc.*;
 import org.sbgn.bindings.Map;
+import org.xml.sax.SAXException;
 
 import lcsb.mapviewer.common.comparator.DoubleComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.geometry.ColorParser;
+import lcsb.mapviewer.converter.ConverterException;
 import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SpeciesConverter;
 import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
 import lcsb.mapviewer.model.graphics.ArrowType;
@@ -86,22 +95,30 @@ public class SbgnmlXmlExporter {
    */
   private java.util.Map<String, Object> sourceTargetMap;
 
+  RenderInformation renderInformation;
+
+  ColorParser colorParser = new ColorParser();
+
   /**
    * Transforms model into SBGN-ML xml.
    * 
    * @param model
    *          model that should be transformed
    * @return SBGM-ML xml string for the model
+   * @throws ConverterException
    */
-  public Sbgn toSbgnml(Model model) {
+  public Sbgn toSbgnml(Model model) throws ConverterException {
     // Reset global variables
     arcCounter = 0;
     parsedOperators = new HashSet<>();
     operatorIds = new HashMap<>();
     sourceTargetMap = new HashMap<>();
+    renderInformation = new RenderInformation();
 
     Map map = new Map();
+    map.setId(model.getIdModel());
     map.setLanguage(Language.PD.getName());
+
     Sbgn sbgnData = new Sbgn();
 
     for (Element element : model.getElements()) {
@@ -131,6 +148,11 @@ public class SbgnmlXmlExporter {
       }
       map.getArc().addAll(getArcsFromReaction(reaction, map.getGlyph()));
     }
+    try {
+      RenderUtil.setRenderInformation(map, renderInformation);
+    } catch (XMLStreamException | JAXBException | ParserConfigurationException | SAXException | IOException e) {
+      throw new ConverterException("Problem with providing render information");
+    }
 
     sbgnData.getMap().add(map);
     return sbgnData;
@@ -191,11 +213,35 @@ public class SbgnmlXmlExporter {
         }
       }
     }
+    addRenderInformation(newGlyph, element);
 
     sourceTargetMap.put(newGlyph.getId(), newGlyph);
     return newGlyph;
   }
 
+  private void addRenderInformation(Glyph glyph, Element element) {
+    float lineWidth = 1.0f;
+    if (element instanceof Species) {
+      lineWidth = ((Species) element).getLineWidth().floatValue();
+    } else if (element instanceof Compartment) {
+      lineWidth = (float) ((Compartment) element).getThickness();
+    }
+    RenderUtil.addStyle(renderInformation, glyph.getId(), colorParser.colorToHtml(element.getFillColor()),
+        colorParser.colorToHtml(element.getBorderColor()), lineWidth);
+  }
+
+  private void addRenderInformation(Glyph glyph, PolylineData line) {
+    float lineWidth = (float) line.getWidth();
+    RenderUtil.addStyle(renderInformation, glyph.getId(), colorParser.colorToHtml(Color.WHITE),
+        colorParser.colorToHtml(line.getColor()), lineWidth);
+  }
+
+  private void addRenderInformation(Arc arc, PolylineData line) {
+    float lineWidth = (float) line.getWidth();
+    RenderUtil.addStyle(renderInformation, arc.getId(), colorParser.colorToHtml(Color.WHITE),
+        colorParser.colorToHtml(line.getColor()), lineWidth);
+  }
+
   private Glyph createStateVariableForStructuralState(StructuralState structuralState) {
     Glyph glyph = new Glyph();
     glyph.setId(structuralState.getSpecies().getElementId() + "-state");
@@ -611,6 +657,8 @@ public class SbgnmlXmlExporter {
 
     sourceTargetMap.put(processGlyph.getId(), processGlyph);
 
+    addRenderInformation(processGlyph, reaction.getLine());
+
     return processGlyph;
   }
 
@@ -922,6 +970,7 @@ public class SbgnmlXmlExporter {
       arc.getNext().add(next);
     }
 
+    addRenderInformation(arc, node.getLine());
     return arc;
   }
 

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

@@ -16,6 +16,7 @@ import org.sbgn.bindings.Map;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.comparator.DoubleComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.geometry.ColorParser;
 import lcsb.mapviewer.common.geometry.PointTransformation;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.converter.ZIndexPopulator;
@@ -81,6 +82,10 @@ public class SbgnmlXmlParser {
 
   Model model;
 
+  RenderInformation renderInformation;
+
+  ColorParser colorParser = new ColorParser();
+
   /**
    * Method used to create a model from SBGN-ML file.
    *
@@ -99,6 +104,7 @@ public class SbgnmlXmlParser {
     model.setIdModel(filename);
 
     Sbgn sbgnData;
+    Map map;
     // Check if input file has valid SBGN-ML data
     try {
       if (!SbgnUtil.isValid(inputSbgnmlFile)) {
@@ -107,13 +113,17 @@ public class SbgnmlXmlParser {
 
       // Read data from file
       sbgnData = SbgnUtil.readFromFile(inputSbgnmlFile);
+      renderInformation = RenderUtil.getRenderInformation(sbgnData);
+      // Extract map with all the glyphs and arcs
+      map = sbgnData.getMap().get(0);
+      if (renderInformation == null) {
+        renderInformation = RenderUtil.getRenderInformation(map);
+      }
+
     } catch (Exception ex) {
       throw new InvalidInputDataExecption("Unable to read given file.", ex);
     }
 
-    // Extract map with all the glyphs and arcs
-    Map map = sbgnData.getMap().get(0);
-
     adjustSizeOfElements(map);
 
     setModelSize(map, model);
@@ -542,6 +552,9 @@ public class SbgnmlXmlParser {
     reaction.addReactant(reactant);
     reaction.addProduct(product);
 
+    assignRenderInformation(reaction.getLine(), arc);
+    assignRenderInformation(reactant.getLine(), arc);
+    assignRenderInformation(product.getLine(), arc);
     model.addReaction(reaction);
   }
 
@@ -702,9 +715,66 @@ public class SbgnmlXmlParser {
       }
     }
 
+    assignRenderInformation(species, glyph);
     model.addElement(species);
   }
 
+  private void assignRenderInformation(Element element, Glyph glyph) {
+    if (renderInformation != null) {
+      Style style = RenderUtil.getStyle(renderInformation, glyph);
+      if (style != null) {
+        try {
+          element.setFillColor(colorParser.parse(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()));
+        } catch (InvalidArgumentException e) {
+          logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, element),
+              "Invalid border color: " + style.getG().getStroke());
+        }
+        if (style.getG().getStrokeWidth() != null) {
+          if (element instanceof Species) {
+            ((Species) element).setLineWidth((double) style.getG().getStrokeWidth());
+          } else if (element instanceof Compartment) {
+            ((Compartment) element).setThickness((double) style.getG().getStrokeWidth());
+          }
+        }
+      }
+    }
+  }
+
+  private void assignRenderInformation(PolylineData line, Arc glyph) {
+    if (renderInformation != null) {
+      Style style = RenderUtil.getStyle(renderInformation, glyph);
+      assignRenderInformation(line, style);
+    }
+  }
+
+  private void assignRenderInformation(PolylineData line, Style style) {
+    if (style != null) {
+      try {
+        Color color = colorParser.parse(style.getG().getStroke());
+        line.setColor(color);
+      } catch (InvalidArgumentException e) {
+        logger.warn("Invalid border color: " + style.getG().getStroke());
+      }
+      if (style.getG().getStrokeWidth() != null) {
+        double lineWidth = (double) style.getG().getStrokeWidth();
+        line.setWidth(lineWidth);
+      }
+    }
+  }
+
+  private void assignRenderInformation(PolylineData line, Glyph glyph) {
+    if (renderInformation != null) {
+      Style style = RenderUtil.getStyle(renderInformation, glyph);
+      assignRenderInformation(line, style);
+    }
+  }
+
   /**
    * Finds a compartment where element should be located (base on the
    * coordinates).
@@ -1200,11 +1270,10 @@ public class SbgnmlXmlParser {
           p.getCentralPoint().getId() + ": The process must have at least one incoming arc.");
     }
 
-    Reaction reaction;
     if (p.getCentralPoint() == null) {
       throw new InvalidArgumentException("Process has no central point.");
     }
-    reaction = getReactionFromProcessGlyphClazz(p.getCentralPoint().getClazz());
+    Reaction reaction = getReactionFromProcessGlyphClazz(p.getCentralPoint().getClazz());
     reaction.setIdReaction(p.getCentralPoint().getId());
     reaction.setModel(model);
 
@@ -1238,6 +1307,7 @@ public class SbgnmlXmlParser {
       }
 
       reaction.addReactant(reactant);
+      assignRenderInformation(reactant.getLine(), a);
     }
 
     for (Arc a : p.getProductArcs()) {
@@ -1252,6 +1322,7 @@ public class SbgnmlXmlParser {
         if (splitOperator != null) {
           splitOperator.addOutput(product);
         }
+        assignRenderInformation(product.getLine(), a);
         reaction.addProduct(product);
       } else {
         Reactant reactant = new Reactant();
@@ -1266,6 +1337,7 @@ public class SbgnmlXmlParser {
           andOperator.addInput(reactant);
         }
 
+        assignRenderInformation(reactant.getLine(), a);
         reaction.addReactant(reactant);
       }
     }
@@ -1333,7 +1405,15 @@ public class SbgnmlXmlParser {
           logger.warn(ex.getMessage());
         }
       }
+      assignRenderInformation(modifier.getLine(), a);
+    }
 
+    assignRenderInformation(reaction.getLine(), p.getCentralPoint());
+    if (andOperator != null) {
+      assignRenderInformation(andOperator.getLine(), p.getCentralPoint());
+    }
+    if (splitOperator != null) {
+      assignRenderInformation(splitOperator.getLine(), p.getCentralPoint());
     }
 
     model.addReaction(reaction);
@@ -1560,6 +1640,7 @@ public class SbgnmlXmlParser {
           compartment.getY() + compartment.getThickness() + CONTAINER_NAME_MARGIN);
     }
 
+    assignRenderInformation(compartment, glyph);
     model.addElement(compartment);
   }
 }

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

@@ -3,7 +3,6 @@ package lcsb.mapviewer.converter.model.sbgnml;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
 
-import java.awt.Color;
 import java.io.File;
 import java.io.FileInputStream;
 import java.util.HashSet;
@@ -19,10 +18,8 @@ import lcsb.mapviewer.common.comparator.StringComparator;
 import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.Drawable;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Protein;
 import lcsb.mapviewer.model.map.species.field.ModificationResidue;

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

+package lcsb.mapviewer.converter.model.sbgnml;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.*;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.converter.Converter;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.Drawable;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Species;
+
+@RunWith(Parameterized.class)
+public class SbgnmlSerializationTest extends SbgnmlTestFunctions {
+
+  Logger logger = LogManager.getLogger();
+
+  private Path filePath;
+
+  public SbgnmlSerializationTest(Path filePath) {
+    this.filePath = filePath;
+  }
+
+  @Parameters(name = "{index} : {0}")
+  public static Collection<Object[]> data() throws IOException {
+    Collection<Object[]> data = new ArrayList<Object[]>();
+    Files.walk(Paths.get("testFiles/CellDesigner-serializable")).forEach(fPath -> {
+      if (Files.isRegularFile(fPath)) {
+        data.add(new Object[] { fPath });
+      }
+    });
+    return data;
+  }
+
+  @Test
+  public void modelSerialization() throws Exception {
+    Converter converter = new CellDesignerXmlParser();
+    Converter sbgnmlConverter = new SbgnmlXmlConverter();
+
+    Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
+
+    String sbgn = sbgnmlConverter.model2String(model);
+    Model model2 = sbgnmlConverter.createModel(
+        new ConverterParams().inputStream(new ByteArrayInputStream(sbgn.getBytes(StandardCharsets.UTF_8))));
+
+    model2.setIdModel(model.getIdModel());
+    model2.setName(model.getName());
+    for (Drawable d : model.getDrawables()) {
+      d.setZ(null);
+    }
+    for (Drawable d : model2.getDrawables()) {
+      d.setZ(null);
+    }
+    for (Species e: model.getSpeciesList()) {
+      e.setInitialAmount(null);
+      e.setInitialConcentration(null);
+      e.setCharge(null);
+      e.setPositionToCompartment(null);
+    }
+    model.getUnits().clear();
+    
+    for (Species e: model2.getSpeciesList()) {
+      e.setInitialAmount(null);
+      e.setInitialConcentration(null);
+      e.setCharge(null);
+      e.setPositionToCompartment(null);
+    }
+    
+    assertEquals("Import/export shouldn't produce any wanrnings", 0, super.getWarnings().size());
+    ModelComparator mc = new ModelComparator(0.001);
+    assertEquals(0, mc.compare(model, model2));
+  }
+
+}

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

@@ -27,7 +27,7 @@ import lcsb.mapviewer.model.map.reaction.ReactionComparator;
 @RunWith(Parameterized.class)
 public class SbgnmlXmlParserTest extends SbgnmlTestFunctions {
 
-  Logger logger = LogManager.getLogger(SbgnmlXmlParserTest.class.getName());
+  Logger logger = LogManager.getLogger();
 
   private Path filePath;