Merge branch '487-custom-images-as-overlay-levels-or-background' into 'master'

Resolve "Custom images as overlay levels  or background"

Closes #487

See merge request minerva/core!768

CHANGELOG

@@ -3,6 +3,9 @@ minerva (13.1.0~alpha.0) unstable; urgency=low
     outputs used by annotator (#617)
   * Feature: changes in admin panel doesn't require saving - they are saved
     automatically (#676)
+  * Feature: elements can have custom glyphs used for visualization (#487)
+  * Small improvement: all bio entities have z-index associated with them 
+    (#487)
   * Small improvement: validation of the organism and disease id on map upload
     added (#618)
   * Small improvement: added current username next to logout button in admin
@@ -48,6 +51,8 @@ minerva (13.1.0~alpha.0) unstable; urgency=low
   * Small improvement: allow admin to disable CORS check (#802)
   * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
     SemanticZoomLevelTransparency (#801)
+  * Small improvement: export/import from SBML support z-index in LAYOUT 
+    extension
   * Bug fix: progress bar of gene genome mapping upload is refreshing properly
     (#728)
   * Bug fix: when editing project Disease and Organism could not be removed

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

@@ -8,7 +8,10 @@ import org.apache.log4j.Logger;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 
 public abstract class Comparator<T extends Object> implements java.util.Comparator<T> {
-  Logger logger = Logger.getLogger(Comparator.class);
+  /**
+   * Default class logger.
+   */
+  private static Logger logger = Logger.getLogger(Comparator.class);
   private Class<T> comparatorClazz;
   private boolean exactClassMatch;
   private List<Comparator<? extends T>> subClassComparatorList = new ArrayList<>();

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

@@ -10,18 +10,18 @@ import java.util.Comparator;
  */
 public class IntegerComparator implements Comparator<Integer> {
 
-	@Override
-	public int compare(Integer arg0, Integer arg1) {
-		if (arg0 == null) {
-			if (arg1 == null) {
-				return 0;
-			} else {
-				return 1;
-			}
-		} else if (arg1 == null) {
-			return -1;
-		}
-		return arg0.compareTo(arg1);
-	}
+  @Override
+  public int compare(Integer arg0, Integer arg1) {
+    if (arg0 == null) {
+      if (arg1 == null) {
+        return 0;
+      } else {
+        return 1;
+      }
+    } else if (arg1 == null) {
+      return -1;
+    }
+    return arg0.compareTo(arg1);
+  }
 
 }

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

@@ -22,6 +22,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.ZIndexPopulator;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.alias.AliasCollectionXmlParser;
 import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
@@ -144,7 +145,10 @@ public class CellDesignerXmlParser extends Converter {
       }
       // we ignore metaid - it's useless and obstruct data model
       // model.setMetaId(XmlParser.getNodeAttr("metaId", modelNode));
-      model.setIdModel(XmlParser.getNodeAttr("id", modelNode));
+      String modelId = XmlParser.getNodeAttr("id", modelNode);
+      if (modelId != null && !modelId.isEmpty()) {
+        model.setIdModel(modelId);
+      }
 
       Node compartmentNode = XmlParser.getNode("listOfCompartments", modelNode.getChildNodes());
       if (compartmentNode != null) {
@@ -236,6 +240,7 @@ public class CellDesignerXmlParser extends Converter {
         model.setWidth(width);
         model.setHeight(height);
       }
+      new ZIndexPopulator().populateZIndex(model);
     } catch (InvalidXmlSchemaException e) {
       throw new InvalidInputDataExecption(e);
     } catch (CellDesignerParserException e) {
@@ -610,7 +615,11 @@ public class CellDesignerXmlParser extends Converter {
           + "xmlns:celldesigner=\"http://www.sbml.org/2001/ns/celldesigner\" level=\"2\" version=\"4\">\n");
       // metaid is a string cell designer id, usually it's model id and as far as
       // we can tell it's not used at all
-      result.append("<model metaid=\"" + model.getIdModel() + "\" id=\"" + model.getIdModel() + "\">\n");
+      result.append("<model ");
+      if (model.getIdModel() != null) {
+        result.append("metaid=\"" + model.getIdModel() + "\" id=\"" + model.getIdModel() + "\"");
+      }
+      result.append(">\n");
 
       result.append(unitCollectionXmlParser.toXml(model.getUnits()));
       result.append(functionCollectionXmlParser.toXml(model.getFunctions()));
@@ -697,7 +706,8 @@ public class CellDesignerXmlParser extends Converter {
 
     result.append("</celldesigner:extension>\n");
     XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
-    result.append(xmlAnnotationParser.dataSetToXmlString(model.getMiriamData(), model.getAuthors(), model.getCreationDate(), model.getModificationDates()));
+    result.append(xmlAnnotationParser.dataSetToXmlString(model.getMiriamData(), model.getAuthors(),
+        model.getCreationDate(), model.getModificationDates()));
     result.append("</annotation>\n");
     return result.toString();
   }

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

@@ -3,7 +3,7 @@ package lcsb.mapviewer.converter.model.celldesigner;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 
 /**
- * Exception that shold be thrown when the group in xml schema is invalid.
+ * Exception that should be thrown when the group in xml schema is invalid.
  * 
  * @author Piotr Gawron
  * 
@@ -20,7 +20,7 @@ public class InvalidGroupException extends InvalidXmlSchemaException {
 	 */
 
 	public InvalidGroupException() {
-		super(); // call superclass constructor
+		super();
 	}
 
 	/**

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

@@ -13,6 +13,7 @@ import org.w3c.dom.NodeList;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.common.geometry.ColorParser;
+import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
 import lcsb.mapviewer.model.graphics.ArrowType;
 import lcsb.mapviewer.model.graphics.LineType;
 import lcsb.mapviewer.model.graphics.PolylineData;
@@ -522,6 +523,7 @@ public class LayerXmlParser {
         }
       }
     }
+    new RestAnnotationParser().processNotes(result.getNotes(), result);
     return result;
   }
 

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

+package lcsb.mapviewer.converter.model.celldesigner.annotation;
+
+import static java.lang.annotation.ElementType.FIELD;
+import static java.lang.annotation.RetentionPolicy.RUNTIME;
+
+import java.lang.annotation.Retention;
+import java.lang.annotation.Target;
+
+@Retention(RUNTIME)
+@Target(FIELD)
+public @interface ImportOnly {
+
+}

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

 package lcsb.mapviewer.converter.model.celldesigner.annotation;
 
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
 import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.Drawable;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
@@ -15,193 +14,197 @@ import lcsb.mapviewer.model.map.species.Species;
  * 
  */
 public enum NoteField {
-	/**
-	 * List of {@link MiriamType#HGNC} identifiers.
-	 */
-	HGNC("HGNC_ID", BioEntity.class, MiriamType.HGNC),
-
-	/**
-	 * List of {@link MiriamType#REFSEQ} identifiers.
-	 */
-	REFSEQ("RefSeq_ID", BioEntity.class, MiriamType.REFSEQ),
-
-	/**
-	 * List of {@link MiriamType#ENTREZ} identifiers.
-	 */
-	ENTREZ("EntrezGene_ID", BioEntity.class, MiriamType.ENTREZ),
-
-	/**
-	 * List of {@link MiriamType#REACTOME} identifiers.
-	 */
-	REACTOME("Reactome_ID", BioEntity.class, MiriamType.REACTOME),
-
-	/**
-	 * List of {@link MiriamType#PUBMED} identifiers.
-	 */
-	PUBMED("Pubmed_ID", BioEntity.class, MiriamType.PUBMED),
-
-	/**
-	 * List of {@link MiriamType#KEGG_GENES} identifiers.
-	 */
-	KEGG_GENES("KEGG_ID", BioEntity.class, MiriamType.KEGG_GENES),
-
-	/**
-	 * List of {@link MiriamType#PANTHER} identifiers.
-	 */
-	PANTHER("PANTHER", BioEntity.class, MiriamType.PANTHER),
-
-	/**
-	 * {@link Element#symbol}.
-	 */
-	SYMBOL("Symbol", CellDesignerElement.class, null),
-
-	/**
-	 * {@link Element#fullName}.
-	 */
-	NAME("Name", CellDesignerElement.class, null),
-
-	/**
-	 * {@link Element#notes} or {@link Reaction#notes} .
-	 */
-	DESCRIPTION("Description", BioEntity.class, null),
-
-	/**
-	 * {@link Element#formerSymbols}.
-	 */
-	PREVIOUS_SYMBOLS("Previous Symbols", CellDesignerElement.class, null),
-
-	/**
-	 * {@link Element#synonyms} or {@link Reaction#synonyms}.
-	 */
-	SYNONYMS("Synonyms", BioEntity.class, null),
-
-	/**
-	 * {@link Element#abbreviation} or {@link Reaction#abbreviation}.
-	 */
-	ABBREVIATION("Abbreviation", BioEntity.class, null),
-
-	/**
-	 * {@link Reaction#formula}.
-	 */
-	FORMULA("Formula", Reaction.class, null),
-
-	/**
-	 * {@link Reaction#mechanicalConfidenceScore}.
-	 */
-	MECHANICAL_CONFIDENCE_SCORE("MechanicalConfidenceScore", Reaction.class, null),
-
-	/**
-	 * {@link Reaction#lowerBound}.
-	 */
-	LOWER_BOUND("LowerBound", Reaction.class, null),
-
-	/**
-	 * {@link Reaction#upperBound}.
-	 */
-	UPPER_BOUND("UpperBound", Reaction.class, null),
-
-	/**
-	 * {@link Reaction#subsystem}.
-	 */
-	SUBSYSTEM("Subsystem", Reaction.class, null),
-
-	/**
-	 * {@link Reaction#geneProteinReaction}.
-	 */
-	GENE_PROTEIN_REACTION("GeneProteinReaction", Reaction.class, null),
-
-	/**
-	 * {@link Element#formula}.
-	 */
-	CHARGED_FORMULA("ChargedFormula", CellDesignerElement.class, null),
-
-	/**
-	 * {@link Species#charge}.
-	 */
-	CHARGE("Charge", CellDesignerSpecies.class, null),
-
-	/**
-	 * {@link Element#getSemanticZoomLevelVisibility()}.
-	 */
-    SEMANTIC_ZOOM_LEVEL_VISIBILITY("SemanticZoomLevelVisibility", BioEntity.class, null),
-    
-    /**
-     * {@link Element#getSemanticZoomLevelVisibility()}.
-     */
-    TRANSPARENCY_ZOOM_LEVEL_VISIBILITY("SemanticZoomLevelTransparency", Element.class, null),
-
-    /**
-     * {@link Element#getSemanticZoomLevelVisibility()}.
-     */
-    @Deprecated
-    TRANSPARENCY_ZOOM_LEVEL_VISIBILITY_OLD("TransparencyZoomLevelVisibility", Element.class, null),
-	;
-
-	/**
-	 * Name used in the notes to distinguish fields.
-	 */
-	private String		 commonName;
-
-	/**
-	 * What object class can have this field.
-	 */
-	private Class<?>	 clazz;
-
-	/**
-	 * What {@link MiriamType} is associated with the field.
-	 */
-	private MiriamType miriamType;
-
-	/**
-	 * Default constructor.
-	 * 
-	 * @param name
-	 *          {@link #commonName}
-	 * @param clazz
-	 *          {@link #clazz}
-	 */
-	NoteField(String name, Class<?> clazz) {
-		this.commonName = name;
-		this.clazz = clazz;
-	}
-
-	/**
-	 * Default constructor.
-	 * 
-	 * @param name
-	 *          {@link #commonName}
-	 * @param clazz
-	 *          {@link #clazz}
-	 * @param type
-	 *          {@link #miriamType}
-	 */
-	NoteField(String name, Class<?> clazz, MiriamType type) {
-		this(name, clazz);
-		this.miriamType = type;
-	}
-
-	/**
-	 * @return the miriamType
-	 * @see #miriamType
-	 */
-	public MiriamType getMiriamType() {
-		return miriamType;
-	}
-
-	/**
-	 * @return the commonName
+  /**
+   * List of {@link MiriamType#HGNC} identifiers.
+   */
+  HGNC("HGNC_ID", BioEntity.class, MiriamType.HGNC),
+
+  /**
+   * List of {@link MiriamType#REFSEQ} identifiers.
+   */
+  REFSEQ("RefSeq_ID", BioEntity.class, MiriamType.REFSEQ),
+
+  /**
+   * List of {@link MiriamType#ENTREZ} identifiers.
+   */
+  ENTREZ("EntrezGene_ID", BioEntity.class, MiriamType.ENTREZ),
+
+  /**
+   * List of {@link MiriamType#REACTOME} identifiers.
+   */
+  REACTOME("Reactome_ID", BioEntity.class, MiriamType.REACTOME),
+
+  /**
+   * List of {@link MiriamType#PUBMED} identifiers.
+   */
+  PUBMED("Pubmed_ID", BioEntity.class, MiriamType.PUBMED),
+
+  /**
+   * List of {@link MiriamType#KEGG_GENES} identifiers.
+   */
+  KEGG_GENES("KEGG_ID", BioEntity.class, MiriamType.KEGG_GENES),
+
+  /**
+   * List of {@link MiriamType#PANTHER} identifiers.
+   */
+  PANTHER("PANTHER", BioEntity.class, MiriamType.PANTHER),
+
+  /**
+   * {@link Element#symbol}.
+   */
+  SYMBOL("Symbol", BioEntity.class, null),
+
+  /**
+   * {@link Element#fullName}.
+   */
+  NAME("Name", BioEntity.class, null),
+
+  /**
+   * {@link Element#notes} or {@link Reaction#notes} .
+   */
+  DESCRIPTION("Description", BioEntity.class, null),
+
+  /**
+   * {@link Element#formerSymbols}.
+   */
+  PREVIOUS_SYMBOLS("Previous Symbols", Element.class, null),
+
+  /**
+   * {@link Element#synonyms} or {@link Reaction#synonyms}.
+   */
+  SYNONYMS("Synonyms", BioEntity.class, null),
+
+  /**
+   * {@link Element#abbreviation} or {@link Reaction#abbreviation}.
+   */
+  ABBREVIATION("Abbreviation", BioEntity.class, null),
+
+  /**
+   * {@link Reaction#formula}.
+   */
+  FORMULA("Formula", Reaction.class, null),
+
+  /**
+   * {@link Reaction#mechanicalConfidenceScore}.
+   */
+  MECHANICAL_CONFIDENCE_SCORE("MechanicalConfidenceScore", Reaction.class, null),
+
+  /**
+   * {@link Reaction#lowerBound}.
+   */
+  LOWER_BOUND("LowerBound", Reaction.class, null),
+
+  /**
+   * {@link Reaction#upperBound}.
+   */
+  UPPER_BOUND("UpperBound", Reaction.class, null),
+
+  /**
+   * {@link Reaction#subsystem}.
+   */
+  SUBSYSTEM("Subsystem", Reaction.class, null),
+
+  /**
+   * {@link Reaction#geneProteinReaction}.
+   */
+  GENE_PROTEIN_REACTION("GeneProteinReaction", Reaction.class, null),
+
+  /**
+   * {@link Element#formula}.
+   */
+  CHARGED_FORMULA("ChargedFormula", Element.class, null),
+
+  /**
+   * {@link Species#charge}.
+   */
+  CHARGE("Charge", Species.class, null),
+
+  /**
+   * {@link Element#getSemanticZoomLevelVisibility()}.
+   */
+  SEMANTIC_ZOOM_LEVEL_VISIBILITY("SemanticZoomLevelVisibility", BioEntity.class, null),
+
+  /**
+   * {@link Element#getSemanticZoomLevelVisibility()}.
+   */
+  TRANSPARENCY_ZOOM_LEVEL_VISIBILITY("SemanticZoomLevelTransparency", Element.class, null),
+
+  /**
+   * {@link Element#getSemanticZoomLevelVisibility()}.
+   */
+  @Deprecated
+  TRANSPARENCY_ZOOM_LEVEL_VISIBILITY_OLD("TransparencyZoomLevelVisibility", Element.class, null),
+
+  @ImportOnly
+  Z_INDEX("Z-Index", Drawable.class, null),
+
+  ;
+
+  /**
+   * Name used in the notes to distinguish fields.
+   */
+  private String commonName;
+
+  /**
+   * What object class can have this field.
+   */
+  private Class<? extends Drawable> clazz;
+
+  /**
+   * What {@link MiriamType} is associated with the field.
+   */
+  private MiriamType miriamType;
+
+  /**
+   * Default constructor.
+   * 
+   * @param name
+   *          {@link #commonName}
+   * @param clazz
+   *          {@link #clazz}
+   */
+  NoteField(String name, Class<? extends Drawable> clazz) {
+    this.commonName = name;
+    this.clazz = clazz;
+  }
+
+  /**
+   * Default constructor.
+   * 
+   * @param name
+   *          {@link #commonName}
+   * @param clazz
+   *          {@link #clazz}
+   * @param type
+   *          {@link #miriamType}
+   */
+  NoteField(String name, Class<? extends Drawable> clazz, MiriamType type) {
+    this(name, clazz);
+    this.miriamType = type;
+  }
+
+  /**
+   * @return the miriamType
+   * @see #miriamType
+   */
+  public MiriamType getMiriamType() {
+    return miriamType;