Merge branch 'gpml-prototype' into 'master'

Gpml prototype

Closes #959

See merge request !990

CHANGELOG

 minerva (15.0.0~alpha.0) stable; urgency=medium
   * Improvement: logs provided for validation data model are structurized (#325)
+  * Improvement: import/export of GPML implemented
   * Small improvement: compartments in not layouted SBML file are more
     scattered (#326) 
   * Small improvement: when downloading a map results in too big file (>1MB)

commons/src/main/java/lcsb/mapviewer/common/Pair.java

@@ -78,7 +78,9 @@ public class Pair<L, R> implements Serializable {
 
   @Override
   public String toString() {
-    return "Pair: " + getLeft().toString() + ", " + getRight().toString();
+    String left = getLeft() == null ? "null" : getLeft().toString();
+    String right = getRight() == null ? "null" : getRight().toString();
+    return "Pair: " + left + ", " + right;
   }
 
 }
\ No newline at end of file

commons/src/main/java/lcsb/mapviewer/common/comparator/AbstractComparator.java

+package lcsb.mapviewer.common.comparator;
+
+import java.util.Comparator;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+public abstract class AbstractComparator<T> implements Comparator<T> {
+  private Logger logger = LogManager.getLogger();
+
+  public int compare(T o1, T o2, String objectName) {
+    int result = compare(o1, o2);
+    if (result != 0) {
+      logger.debug(objectName + " different: " + o1 + "\t" + o2);
+    }
+    return result;
+  }
+}

commons/src/main/java/lcsb/mapviewer/common/comparator/ColorComparator.java

 package lcsb.mapviewer.common.comparator;
 
-import java.awt.*;
-import java.util.Comparator;
+import java.awt.Color;
 
 /**
  * Comparator implementation for {@link Color} class.
@@ -9,7 +8,7 @@ import java.util.Comparator;
  * @author Piotr Gawron
  * 
  */
-public class ColorComparator implements Comparator<Color> {
+public class ColorComparator extends AbstractComparator<Color> {
 
   @Override
   public int compare(Color arg0, Color arg1) {

commons/src/main/java/lcsb/mapviewer/common/comparator/DoubleComparator.java

 package lcsb.mapviewer.common.comparator;
 
-import java.util.Comparator;
-
 import lcsb.mapviewer.common.Configuration;
 
 /**
@@ -10,7 +8,7 @@ import lcsb.mapviewer.common.Configuration;
  * @author Piotr Gawron
  * 
  */
-public class DoubleComparator implements Comparator<Double> {
+public class DoubleComparator extends AbstractComparator<Double> {
 
   /**
    * Epsilon value used for comparison of doubles.

commons/src/main/java/lcsb/mapviewer/common/comparator/IntegerComparator.java

 package lcsb.mapviewer.common.comparator;
 
-import java.util.Comparator;
-
 /**
  * Comparator implemented for {@link Integer} class.
  * 
  * @author Piotr Gawron
  * 
  */
-public class IntegerComparator implements Comparator<Integer> {
+public class IntegerComparator extends AbstractComparator<Integer> {
 
   @Override
   public int compare(Integer arg0, Integer arg1) {

commons/src/main/java/lcsb/mapviewer/common/comparator/StringComparator.java

 package lcsb.mapviewer.common.comparator;
 
-import java.util.Comparator;
-
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
@@ -12,7 +10,7 @@ import org.apache.logging.log4j.Logger;
  * @author Piotr Gawron
  * 
  */
-public class StringComparator implements Comparator<String> {
+public class StringComparator extends AbstractComparator<String> {
   /**
    * Default class logger.
    */

converter-CellDesigner/pom.xml

@@ -67,6 +67,13 @@
 			<scope>compile</scope>
 		</dependency>
 
+		<!-- https://mvnrepository.com/artifact/org.springframework/spring-context -->
+		<dependency>
+			<groupId>org.springframework</groupId>
+			<artifactId>spring-context</artifactId>
+			<version>${springframework.version}</version>
+		</dependency>
+
 	</dependencies>
 
 </project>
\ No newline at end of file

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

@@ -11,6 +11,7 @@ import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.core.LogEvent;
 import org.apache.xerces.parsers.DOMParser;
+import org.springframework.stereotype.Component;
 import org.w3c.dom.*;
 
 import lcsb.mapviewer.common.*;
@@ -55,6 +56,7 @@ import lcsb.mapviewer.model.map.species.Element;
  * @author Piotr Gawron
  * 
  */
+@Component
 public class CellDesignerXmlParser extends Converter {
 
   /**

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

@@ -9,12 +9,14 @@ import org.apache.commons.text.StringEscapeUtils;
 import org.apache.logging.log4j.core.LogEvent;
 import org.sbgn.SbgnUtil;
 import org.sbgn.bindings.Sbgn;
+import org.springframework.stereotype.Component;
 
 import lcsb.mapviewer.common.MimeType;
 import lcsb.mapviewer.common.MinervaLoggerAppender;
 import lcsb.mapviewer.converter.*;
 import lcsb.mapviewer.model.map.model.Model;
 
+@Component
 public class SbgnmlXmlConverter extends Converter {
 
   @Override

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java

@@ -420,8 +420,8 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
   public void drawText(final T species, final Graphics2D graphics, final ConverterParams params) {
     String text = getText(species);
     Font oldFont = graphics.getFont();
-    Font font = getFont(species, params);
     Color oldColor = graphics.getColor();
+    Font font = getFont(species, params);
     graphics.setColor(species.getFontColor());
     graphics.setFont(font);
 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java

@@ -13,6 +13,7 @@ import org.sbml.jsbml.ext.SBasePlugin;
 import org.sbml.jsbml.ext.layout.Layout;
 import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
 import org.sbml.jsbml.ext.multi.MultiModelPlugin;
+import org.springframework.stereotype.Component;
 
 import lcsb.mapviewer.commands.CommandExecutionException;
 import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
@@ -33,6 +34,7 @@ import lcsb.mapviewer.model.map.species.*;
 import lcsb.mapviewer.model.map.species.field.ModificationResidue;
 import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
 
+@Component
 public class SbmlParser extends Converter {
 
   /**

converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java

@@ -40,7 +40,6 @@ public class ZIndexPopulator {
     int maxZIndex = 0;
 
     List<Drawable> bioEntities = new ArrayList<>();
-    bioEntities.addAll(model.getBioEntities());
     for (Layer layer : model.getLayers()) {
       bioEntities.addAll(layer.getOvals());
       bioEntities.addAll(layer.getRectangles());

model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java

@@ -260,15 +260,17 @@ public class PolylineData implements Serializable, Drawable {
    * @param distToTrim
    *          distance by which end of line should be trimmed
    */
-  public void trimEnd(double distToTrim) {
+  public double trimEnd(double distToTrim) {
     Point2D last = points.get(points.size() - 1);
     Point2D last2 = points.get(points.size() - 2);
     double oldDist = last.distance(last2);
     if (distToTrim < 0 && oldDist <= Configuration.EPSILON) {
       logger.debug("Cannot extend empty line");
       last.setLocation(last2);
+      return 0;
     } else if (oldDist <= distToTrim) {
       last.setLocation(last2);
+      return oldDist;
     } else {
       double newDistr = oldDist - distToTrim;
       double ratio = newDistr / oldDist;
@@ -277,6 +279,7 @@ public class PolylineData implements Serializable, Drawable {
       dx *= ratio;
       dy *= ratio;
       last.setLocation(last2.getX() + dx, last2.getY() + dy);
+      return distToTrim;
     }
   }
 
@@ -286,12 +289,13 @@ public class PolylineData implements Serializable, Drawable {
    * @param distToTrim
    *          distance by which beginning of line should be trimmed
    */
-  public void trimBegin(double distToTrim) {
+  public double trimBegin(double distToTrim) {
     Point2D last = points.get(0);
     Point2D last2 = points.get(1);
     double oldDist = last.distance(last2);
     if (oldDist <= distToTrim) {
       last.setLocation(last2);
+      return oldDist;
     } else {
       double newDistr = oldDist - distToTrim;
       double ratio = newDistr / oldDist;
@@ -300,6 +304,7 @@ public class PolylineData implements Serializable, Drawable {
       dx *= ratio;
       dy *= ratio;
       last.setLocation(last2.getX() + dx, last2.getY() + dy);
+      return distToTrim;
     }
   }
 

model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java

@@ -50,7 +50,7 @@ public class Compartment extends Element {
   /**
    * Default thickness of compartment border.
    */
-  private static final int DEFAULT_COMPARTMENT_THICKNESS = 12;
+  public static final int DEFAULT_COMPARTMENT_THICKNESS = 12;
 
   /**
    * Default class logger.

model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerComparator.java

@@ -6,6 +6,7 @@ import org.apache.logging.log4j.Logger;
 import lcsb.mapviewer.common.Comparator;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.comparator.*;
+import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.graphics.PolylineDataComparator;
 
 /**
@@ -88,40 +89,32 @@ public class LayerComparator extends Comparator<Layer> {
       return integerComparator.compare(arg0.getOvals().size(), arg1.getOvals().size());
     }
 
-    LayerTextComparator textComparator = new LayerTextComparator(epsilon);
-    for (int i = 0; i < arg0.getTexts().size(); i++) {
-      int status = textComparator.compare(arg0.getTexts().get(i), arg1.getTexts().get(i));
-      if (status != 0) {
-        logger.debug("layer texts different");
-        return status;
-      }
+    ListComparator<LayerText> textComparator = new ListComparator<>(new LayerTextComparator(epsilon));
+    int status = textComparator.compare(arg0.getTexts(), arg1.getTexts());
+    if (status != 0) {
+      logger.debug("layer texts different");
+      return status;
     }
 
-    LayerOvalComparator ovalComparator = new LayerOvalComparator(epsilon);
-    for (int i = 0; i < arg0.getOvals().size(); i++) {
-      int status = ovalComparator.compare(arg0.getOvals().get(i), arg1.getOvals().get(i));
-      if (status != 0) {
-        logger.debug("layer ovals different");
-        return status;
-      }
+    ListComparator<LayerOval> ovalComparator = new ListComparator<>(new LayerOvalComparator(epsilon));
+    status = ovalComparator.compare(arg0.getOvals(), arg1.getOvals());
+    if (status != 0) {
+      logger.debug("layer ovals different");
+      return status;
     }
 
-    LayerRectComparator rectComparator = new LayerRectComparator(epsilon);
-    for (int i = 0; i < arg0.getRectangles().size(); i++) {
-      int status = rectComparator.compare(arg0.getRectangles().get(i), arg1.getRectangles().get(i));
-      if (status != 0) {
-        logger.debug("layer rectangles different ");
-        return status;
-      }
+    ListComparator<LayerRect> rectComparator = new ListComparator<>(new LayerRectComparator(epsilon));
+    status = rectComparator.compare(arg0.getRectangles(), arg1.getRectangles());
+    if (status != 0) {
+      logger.debug("layer rectangles different ");
+      return status;
     }
 
-    PolylineDataComparator lineComparator = new PolylineDataComparator(epsilon);
-    for (int i = 0; i < arg0.getLines().size(); i++) {
-      int status = lineComparator.compare(arg0.getLines().get(i), arg1.getLines().get(i));
-      if (status != 0) {
-        logger.debug("layer lines different ");
-        return status;
-      }
+    ListComparator<PolylineData> lineComparator = new ListComparator<>(new PolylineDataComparator(epsilon));
+    status = lineComparator.compare(arg0.getLines(), arg1.getLines());
+    if (status != 0) {
+      logger.debug("layer lines different ");
+      return status;
     }
 
     return 0;

model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerTextComparator.java

 package lcsb.mapviewer.model.map.layout.graphics;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
 import lcsb.mapviewer.common.Comparator;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.comparator.*;
@@ -13,6 +16,8 @@ import lcsb.mapviewer.common.comparator.*;
  */
 public class LayerTextComparator extends Comparator<LayerText> {
 
+  private Logger logger = LogManager.getLogger();
+
   /**
    * Epsilon value used for comparison of doubles.
    */
@@ -44,35 +49,35 @@ public class LayerTextComparator extends Comparator<LayerText> {
     IntegerComparator integerComparator = new IntegerComparator();
 
     if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
-      return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+      return doubleComparator.compare(arg0.getWidth(), arg1.getWidth(), "width");
     }
 
     if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
-      return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
+      return doubleComparator.compare(arg0.getHeight(), arg1.getHeight(), "height");
     }
 
     if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
-      return doubleComparator.compare(arg0.getX(), arg1.getX());
+      return doubleComparator.compare(arg0.getX(), arg1.getX(), "x");
     }
 
     if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
-      return doubleComparator.compare(arg0.getY(), arg1.getY());
+      return doubleComparator.compare(arg0.getY(), arg1.getY(), "y");
     }
 
     if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
-      return colorComparator.compare(arg0.getColor(), arg1.getColor());
+      return colorComparator.compare(arg0.getColor(), arg1.getColor(), "color");
     }
 
     if (stringComparator.compare(arg0.getNotes(), arg1.getNotes()) != 0) {
-      return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
+      return stringComparator.compare(arg0.getNotes(), arg1.getNotes(), "notes");
     }
 
     if (doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize()) != 0) {
-      return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize());
+      return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize(), "fontSize");
     }
 
     if (integerComparator.compare(arg0.getZ(), arg1.getZ()) != 0) {
-      return integerComparator.compare(arg0.getZ(), arg1.getZ());
+      return integerComparator.compare(arg0.getZ(), arg1.getZ(), "z");
     }
 
     return 0;

model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java

@@ -117,7 +117,7 @@ public class ElementComparator extends Comparator<Element> {
     }
 
     if (colorComparator.compare(arg0.getFontColor(), arg1.getFontColor()) != 0) {
-      logger.debug("Border Font different: " + arg0.getFontColor() + ", " + arg1.getFontColor());
+      logger.debug("Font color different: " + arg0.getFontColor() + ", " + arg1.getFontColor());
       return colorComparator.compare(arg0.getFontColor(), arg1.getFontColor());
     }
 

pathvisio/.project

@@ -5,6 +5,11 @@
 	<projects>
 	</projects>
 	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.wst.common.project.facet.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 		<buildCommand>
 			<name>org.eclipse.jdt.core.javabuilder</name>
 			<arguments>
@@ -15,6 +20,11 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.wst.validation.validationbuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 		<buildCommand>
 			<name>org.eclipse.m2e.core.maven2Builder</name>
 			<arguments>
@@ -22,8 +32,11 @@
 		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
+		<nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>net.sf.eclipsecs.core.CheckstyleNature</nature>
+		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
 	</natures>
 </projectDescription>

pathvisio/pom.xml

@@ -8,7 +8,7 @@
   <artifactId>pathvisio</artifactId>
   <name>Pathvisio plugin</name>
   
-  <packaging>bundle</packaging>
+<!--   <packaging>bundle</packaging>
   
 	<build>
 		<plugins>
@@ -128,7 +128,7 @@
 			</plugin>	
 		</plugins>
 	</build>
-
+--> 
 	<repositories>
 		<repository>
    		<id>repo</id>