fix export/import notes (export notes for all bionetities and escape xml)

CHANGELOG

@@ -2,6 +2,8 @@ minerva (15.0.2) stable; urgency=medium
   * Bug fix: annotations using identifiers.org urls sometimes required http and
     sometimes required https url (#1297)
   * Bug fix: map notes were not exported to GPML
+  * Bug fix: reaction notes were not imported from GPML
+  * Bug fix: export of notes could create invalid GPML file (#1299) 
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Jun 2020 11:00:00 +0200
 

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

@@ -131,12 +131,16 @@ public class ModelContructor {
       species.setHypothetical(true);
     }
     species.setName(dataNode.getName());
-    StringBuilder notes = new StringBuilder();
+    species.setNotes(getComments(dataNode));
+    return species;
+  }
+
+  private String getComments(PathwayElement dataNode) {
+    StringBuilder notes = new StringBuilder("");
     for (String comment : dataNode.getComments()) {
       notes.append(comment + "\n\n");
     }
-    species.setNotes(notes.toString());
-    return species;
+    return notes.toString();
   }
 
   /**
@@ -197,7 +201,7 @@ public class ModelContructor {
   protected void addElement(Model model, Graph graph, Data data) {
     for (DataNode dataNode : graph.getDataNodes()) {
       Species species = createSpecies(dataNode);
-      species.addMiriamData(biopaxFactory.getMiriamData(graph.getBiopaxData(), dataNode.getBiopaxReference()));
+      species.addMiriamData(biopaxFactory.getMiriamData(graph.getBiopaxData(), dataNode.getBiopaxReferences()));
 
       Element alias = updateAlias(dataNode, species);
 
@@ -207,7 +211,7 @@ public class ModelContructor {
     for (Label label : graph.getLabels()) {
       if (label.isTreatAsNode()) {
         Species species = createSpecies(label);
-        species.addMiriamData(biopaxFactory.getMiriamData(graph.getBiopaxData(), label.getBiopaxReference()));
+        species.addMiriamData(biopaxFactory.getMiriamData(graph.getBiopaxData(), label.getBiopaxReferences()));
 
         Element alias = updateAlias(label, species);
 
@@ -221,7 +225,7 @@ public class ModelContructor {
     for (Shape shape : graph.getShapes()) {
       if (shape.isTreatAsNode()) {
         Species species = createSpecies(shape);
-        species.addMiriamData(biopaxFactory.getMiriamData(graph.getBiopaxData(), shape.getBiopaxReference()));
+        species.addMiriamData(biopaxFactory.getMiriamData(graph.getBiopaxData(), shape.getBiopaxReferences()));
 
         Element alias = updateAlias(shape, species);
 
@@ -671,6 +675,8 @@ public class ModelContructor {
         reaction.setReversible(true);
       }
     }
+    
+    reaction.setNotes(getComments(interaction));
 
     reaction.addMiriamData(interaction.getReferences());
     reaction.setZ(interaction.getzOrder());

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

@@ -7,6 +7,7 @@ import java.awt.geom.*;
 import java.util.HashSet;
 import java.util.Set;
 
+import org.apache.commons.text.StringEscapeUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
@@ -338,7 +339,7 @@ public class ModelToGPML {
     String shape = ShapeMapping.getShape(ca.getClass()).getStringRepresentation();
 
     comparments.append("  <Shape TextLabel=\"" + ca.getName() + "\" GraphId=\"" + ca.getElementId() + "\">\n");
-    comparments.append("    <Comment>" + getAllNames(ca) + "</Comment>\n");
+    comparments.append("    <Comment>" + StringEscapeUtils.escapeXml11(getAllNames(ca)) + "</Comment>\n");
     comparments.append("    <Attribute Key=\"org.pathvisio.CellularComponentProperty\" Value=\"Cell\" />\n");
     comparments.append("    <Attribute Key=\"org.pathvisio.DoubleLineProperty\" Value=\"Double\" />\n");
     comparments.append(
@@ -531,7 +532,7 @@ public class ModelToGPML {
     }
     result.append(">\n");
 
-    result.append("    <Comment>" + species.getNotes().trim() + "</Comment>\n");
+    result.append("    <Comment>" + StringEscapeUtils.escapeXml11(species.getNotes().trim()) + "</Comment>\n");
     result.append(biopaxParser.toReferenceXml(species.getMiriamData()));
 
     Rectangle2D rec = species.getBorder();
@@ -564,7 +565,7 @@ public class ModelToGPML {
     }
     result.append(">\n");
 
-    result.append("    <Comment>" + species.getNotes().trim() + "</Comment>\n");
+    result.append("    <Comment>" + StringEscapeUtils.escapeXml11(species.getNotes().trim()) + "</Comment>\n");
 
     Rectangle2D rec = species.getBorder();
 
@@ -607,7 +608,7 @@ public class ModelToGPML {
     }
     result.append(">\n");
 
-    result.append("    <Comment>" + species.getNotes() + "</Comment>\n");
+    result.append("    <Comment>" + StringEscapeUtils.escapeXml11(species.getNotes().trim()) + "</Comment>\n");
     result.append(biopaxParser.toReferenceXml(species.getMiriamData()));
 
     Rectangle2D rec = species.getBorder();
@@ -721,6 +722,9 @@ public class ModelToGPML {
 
       interactions.append("  <Interaction GraphId=\"" + reaction.getIdReaction() + "\">\n");
       interactions.append(biopaxParser.toReferenceXml(reaction.getMiriamData()));
+      if (reaction.getNotes() != null) {
+        interactions.append("  <Comment>" + StringEscapeUtils.escapeXml11(reaction.getNotes().trim()) + "</Comment>\n");
+      }
       interactions.append("    <Graphics "
           + "ConnectorType=\"Segmented\" "
           + "ZOrder=\"" + reaction.getZ() + "\" "
@@ -730,6 +734,8 @@ public class ModelToGPML {
       }
       interactions.append("LineThickness=\"" + reaction.getLine().getWidth() + "\">\n");
 
+
+      
       /** Start and End **/
       Reactant start = reaction.getReactants().get(0);
       Product end = reaction.getProducts().get(0);
@@ -806,7 +812,7 @@ public class ModelToGPML {
     gpml.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
     gpml.append("<Pathway xmlns=\"http://pathvisio.org/GPML/2013a\" Name=\"Generated\">\n");
     if (model.getNotes() != null) {
-      gpml.append("  <Comment>" + model.getNotes().trim() + "</Comment>\n");
+      gpml.append("  <Comment>" + StringEscapeUtils.escapeXml11(model.getNotes().trim()) + "</Comment>\n");
     }
     gpml.append("  <Graphics BoardWidth=\"" + model.getWidth() + "\" BoardHeight=\"" + model.getHeight() + "\"/>\n");
 

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Interaction.java

 package lcsb.mapviewer.wikipathway.model;
 
 import java.awt.Color;
+import java.awt.geom.Rectangle2D;
 import java.io.Serializable;
 import java.util.*;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
+import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.MiriamData;
 
@@ -16,7 +18,7 @@ import lcsb.mapviewer.model.map.MiriamData;
  * @author Jan Badura
  * 
  */
-public class Interaction implements Serializable {
+public class Interaction extends PathwayElement implements Serializable {
   static Logger logger = LogManager.getLogger();
 
   /**
@@ -24,11 +26,6 @@ public class Interaction implements Serializable {
    */
   private static final long serialVersionUID = 1L;
 
-  /**
-   * Identifier in GPML model.
-   */
-  private String graphId;
-
   /**
    * Where this {@link Interaction} starts (in which {@link Edge}/
    * {@link Interaction}).
@@ -46,11 +43,6 @@ public class Interaction implements Serializable {
    */
   private PolylineData line;
 
-  /**
-   * Z order of the {@link Interaction} (how far it should be located in the z
-   * coordinate).
-   */
-  private Integer zOrder;
 
   /**
    * Gpml interaction type (arrow).
@@ -62,10 +54,6 @@ public class Interaction implements Serializable {
    */
   private Set<String> anchors;
 
-  /**
-   * Comments.
-   */
-  private List<String> comments = new ArrayList<>();
 
   /**
    * List of edges representing reactants in interaction.
@@ -82,11 +70,6 @@ public class Interaction implements Serializable {
    */
   private Set<Edge> modifiers = new HashSet<>();
 
-  /**
-   * Identifiers of BioPax references.
-   */
-  private Set<String> biopaxReferences = new HashSet<>();
-
   /**
    * References for given edge.
    */
@@ -101,7 +84,7 @@ public class Interaction implements Serializable {
    *          object will be created from this {@link Edge}
    */
   public Interaction(Edge edge) {
-    graphId = edge.getGraphId();
+    super(edge.getGraphId(), null);
     setStart(edge.getStart());
     setEnd(edge.getEnd());
     setLine(edge.getLine());
@@ -111,8 +94,8 @@ public class Interaction implements Serializable {
       addReference(new MiriamData(md));
     }
     setColor(edge.getColor());
-    this.comments.addAll(edge.getComments());
-    biopaxReferences.addAll(edge.getBiopaxReferences());
+    addComments(edge.getComments());
+    addBiopaxReferences(edge.getBiopaxReferences());
     reversible = edge.isReversibleReaction();
   }
 
@@ -133,23 +116,6 @@ public class Interaction implements Serializable {
     references.add(reference);
   }
 
-  /**
-   * @return the graphId
-   * @see #graphId
-   */
-  public String getGraphId() {
-    return graphId;
-  }
-
-  /**
-   * @param graphId
-   *          the graphId to set
-   * @see #graphId
-   */
-  public void setGraphId(String graphId) {
-    this.graphId = graphId;
-  }
-
   /**
    * @return the start
    * @see #start
@@ -218,23 +184,6 @@ public class Interaction implements Serializable {
     this.anchors = anchors;
   }
 
-  /**
-   * @return the comment
-   * @see #comment
-   */
-  public List<String> getComments() {
-    return comments;
-  }
-
-  /**
-   * @param comment
-   *          the comment to set
-   * @see #comment
-   */
-  public void addComment(String comment) {
-    this.comments.add(comment);
-  }
-
   /**
    * @return the reactants
    * @see #reactants
@@ -267,7 +216,7 @@ public class Interaction implements Serializable {
    */
   public void addProduct(Edge interaction) {
     this.products.add(interaction);
-    biopaxReferences.addAll(interaction.getBiopaxReferences());
+    addBiopaxReferences(interaction.getBiopaxReferences());
   }
 
   /**
@@ -278,7 +227,7 @@ public class Interaction implements Serializable {
    */
   public void addModifier(Edge interaction) {
     this.modifiers.add(interaction);
-    biopaxReferences.addAll(interaction.getBiopaxReferences());
+    addBiopaxReferences(interaction.getBiopaxReferences());
   }
 
   /**
@@ -289,24 +238,7 @@ public class Interaction implements Serializable {
    */
   public void addReactant(Edge interaction) {
     this.reactants.add(interaction);
-    biopaxReferences.addAll(interaction.getBiopaxReferences());
-  }
-
-  /**
-   * @return the biopaxReferences
-   * @see #biopaxReferences
-   */
-  public Set<String> getBiopaxReferences() {
-    return biopaxReferences;
-  }
-
-  /**
-   * @param biopaxReferences
-   *          the biopaxReferences to set
-   * @see #biopaxReferences
-   */
-  public void setBiopaxReferences(Set<String> biopaxReferences) {
-    this.biopaxReferences = biopaxReferences;
+    addBiopaxReferences(interaction.getBiopaxReferences());
   }
 
   /**
@@ -371,23 +303,6 @@ public class Interaction implements Serializable {
     }
   }
 
-  /**
-   * @return the zOrder
-   * @see #zOrder
-   */
-  public Integer getzOrder() {
-    return zOrder;
-  }
-
-  /**
-   * @param zOrder
-   *          the zOrder to set
-   * @see #zOrder
-   */
-  public void setzOrder(Integer zOrder) {
-    this.zOrder = zOrder;
-  }
-
   public boolean isReversible() {
     return reversible;
   }
@@ -396,4 +311,14 @@ public class Interaction implements Serializable {
     this.reversible = reversible;
   }
 
+  @Override
+  String getName() {
+    throw new NotImplementedException();
+  }
+
+  @Override
+  Rectangle2D getRectangle() {
+    throw new NotImplementedException();
+  }
+
 }

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java

@@ -2,8 +2,7 @@ package lcsb.mapviewer.wikipathway.model;
 
 import java.awt.geom.Rectangle2D;
 import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
+import java.util.*;
 
 import lcsb.mapviewer.model.LogMarker;
 import lcsb.mapviewer.model.ProjectLogEntryType;
@@ -104,7 +103,7 @@ public abstract class PathwayElement implements Serializable {
    * @return the biopaxReference
    * @see #biopaxReference
    */
-  public List<String> getBiopaxReference() {
+  public List<String> getBiopaxReferences() {
     return biopaxReferences;
   }
 
@@ -113,7 +112,7 @@ public abstract class PathwayElement implements Serializable {
    *          the biopaxReference to set
    * @see #biopaxReference
    */
-  public void setBiopaxReference(List<String> biopaxReferences) {
+  public void setBiopaxReferences(List<String> biopaxReferences) {
     this.biopaxReferences = biopaxReferences;
   }
 
@@ -143,6 +142,10 @@ public abstract class PathwayElement implements Serializable {
   public void addBiopaxReference(String biopaxString) {
     biopaxReferences.add(biopaxString);
   }
+  
+  public void addBiopaxReferences(Collection<String> biopaxStrings) {
+    biopaxReferences.addAll(biopaxStrings);
+  }
 
   /**
    * @return the comments
@@ -161,6 +164,10 @@ public abstract class PathwayElement implements Serializable {
     this.comments.add(comment);
   }
 
+  public void addComments(Collection<String> comments) {
+    this.comments.addAll(comments);
+  }
+
   public String getMapName() {
     return mapName;
   }

pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/DataNodeParserTest.java

@@ -33,8 +33,8 @@ public class DataNodeParserTest extends WikipathwaysTestFunctions {
     assertNotNull(dataNode);
     assertEquals("GeneProduct", dataNode.getTextLabel());
     assertEquals("ab30b", dataNode.getGraphId());
-    assertEquals(1, dataNode.getBiopaxReference().size());
-    assertEquals("aea", dataNode.getBiopaxReference().get(0));
+    assertEquals(1, dataNode.getBiopaxReferences().size());
+    assertEquals("aea", dataNode.getBiopaxReferences().get(0));
     assertEquals(1, dataNode.getReferences().size());
     assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"), dataNode.getReferences().get(0));
 

pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/LabelParserTest.java

@@ -29,8 +29,8 @@ public class LabelParserTest extends WikipathwaysTestFunctions {
 
     assertEquals("Label 2", label.getTextLabel());
     assertEquals("edf06", label.getGraphId());
-    assertEquals(2, label.getBiopaxReference().size());
-    assertEquals("b38", label.getBiopaxReference().get(1));
+    assertEquals(2, label.getBiopaxReferences().size());
+    assertEquals("b38", label.getBiopaxReferences().get(1));
 
     assertEquals((Integer) 28672, label.getzOrder());
     assertEquals((Double) 10.0, label.getFontSize());

pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java

@@ -22,6 +22,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.SquareCompartment;
 import lcsb.mapviewer.model.map.model.*;
 import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
 import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
 import lcsb.mapviewer.model.map.species.*;
 import lcsb.mapviewer.model.map.species.field.ModificationState;
@@ -201,7 +202,7 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
   }
 
   private Reaction createReaction(Species p1, Species p2) {
-    Reaction reaction = new TransportReaction("re" + (speciesCounter++));
+    Reaction reaction = new StateTransitionReaction("re" + (speciesCounter++));
     Reactant reactant = new Reactant(p1);
     Product product = new Product(p2);
     reaction.addReactant(reactant);
@@ -410,4 +411,33 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
 
     assertEquals(0, new ModelComparator().compare(model, model2));
   }
+
+  @Test
+  public void testHtmlTagInNotes() throws Exception {
+    Model model = new ModelFullIndexed(null);
+    model.setWidth(1000);
+    model.setHeight(1000);
+    model.setNotes("a < b");
+
+    
+    Species p1 = createProtein();
+    p1.setNotes("<a href='https://google.lu/'>link</a>");
+
+    model.addElement(p1);
+    
+    Species p2 = createProtein();
+    model.addElement(p2);
+    
+    Reaction r= createReaction(p1, p2);
+    r.setNotes("<xml>tag</xml>");
+    model.addReaction(r);
+
+    lcsb.mapviewer.wikipathway.GpmlParser parser = new lcsb.mapviewer.wikipathway.GpmlParser();
+
+    String xml = parser.model2String(model);
+    Model model2 = parser.createModel(new ConverterParams().inputStream(new ByteArrayInputStream(xml.getBytes())));
+
+    assertEquals(0, new ModelComparator().compare(model, model2));
+  }
+
 }

pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ShapeParserTest.java

@@ -47,8 +47,8 @@ public class ShapeParserTest extends WikipathwaysTestFunctions {
 
     assertEquals("dfdfs fds ", shape.getTextLabel());
     assertEquals("eb55e", shape.getGraphId());
-    assertEquals(1, shape.getBiopaxReference().size());
-    assertEquals("d04", shape.getBiopaxReference().get(0));
+    assertEquals(1, shape.getBiopaxReferences().size());
+    assertEquals("d04", shape.getBiopaxReferences().get(0));
 
     assertEquals((Integer) 16384, shape.getzOrder());
     assertEquals((Double) 10.0, shape.getFontSize());
@@ -69,8 +69,8 @@ public class ShapeParserTest extends WikipathwaysTestFunctions {
 
     assertEquals("compartment title", shape.getTextLabel());
     assertEquals("c5869", shape.getGraphId());
-    assertEquals(1, shape.getBiopaxReference().size());
-    assertEquals("b80", shape.getBiopaxReference().get(0));
+    assertEquals(1, shape.getBiopaxReferences().size());
+    assertEquals("b80", shape.getBiopaxReferences().get(0));
 
     assertEquals((Integer) 16384, shape.getzOrder());
     assertEquals((Double) 10.0, shape.getFontSize());