Merge branch...

Merge branch '2208-bug-in-celldesigner-export-the-default-compartment-is-exported-with-an-empty-string-as-its-name' into 'master'

Resolve "bug in CellDesigner export: the default compartment is exported with an empty string as its name"

See merge request !1870

.aspell-api-exceptions.pws

@@ -305,6 +305,7 @@ ird
 irefweb
 isbn
 isDefault
+isDescribedBy
 isfinder
 isoform
 Isoform

CHANGELOG

 minerva (18.1.1) stable; urgency=medium
   * Bug fix: SBGN-ML import/export should not use compartmentOrder for
     non-compartment entities (#2193)
-  * Bug fix: invalir relation type has been used as default
+  * Bug fix: invalid relation type has been used as default
     (bqbiol:isDescribedBy), the default is changed to: bqbiol:is (#2206)
+  * Bug fix: export of default compartment provide compartment name (#2208)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 05 Feb 2025 12:00:00 +0200
 

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

 package lcsb.mapviewer.converter.model.celldesigner.compartment;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
@@ -18,12 +7,21 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompart
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 
 /**
  * CellDEsigner xml parser for collection of compartments.
- * 
+ *
  * @author Piotr Gawron
- * 
  */
 public class CompartmentCollectionXmlParser {
 
@@ -31,25 +29,24 @@ public class CompartmentCollectionXmlParser {
    * Default class logger.
    */
   @SuppressWarnings("unused")
-  private Logger logger = LogManager.getLogger();
+  private final Logger logger = LogManager.getLogger();
 
   /**
    * CellDesigner xml parser for single compartment.
    */
-  private CompartmentXmlParser compartmentParser;
+  private final CompartmentXmlParser compartmentParser;
 
   /**
    * Collection of {@link CellDesignerElement cell designer elements} parsed from
    * xml.
    */
-  private CellDesignerElementCollection elements;
+  private final CellDesignerElementCollection elements;
 
   /**
    * Default constructor.
-   * 
-   * @param elements
-   *          collection of {@link CellDesignerElement cell designer elements}
-   *          parsed from xml
+   *
+   * @param elements collection of {@link CellDesignerElement cell designer elements}
+   *                 parsed from xml
    */
   public CompartmentCollectionXmlParser(final CellDesignerElementCollection elements) {
     this.elements = elements;
@@ -58,14 +55,11 @@ public class CompartmentCollectionXmlParser {
 
   /**
    * Parse CellDEsigner xml node with collection of compartments.
-   * 
-   * @param compartmentsNode
-   *          xml node to parse
+   *
+   * @param compartmentsNode xml node to parse
    * @return list of compartments obtained from xml node
-   * @throws InvalidXmlSchemaException
-   *           thrown when there is a problem with xml
-   * @throws CompartmentParserException
-   *           thrown when there is a problem with parsing a compartment
+   * @throws InvalidXmlSchemaException  thrown when there is a problem with xml
+   * @throws CompartmentParserException thrown when there is a problem with parsing a compartment
    */
   public List<CellDesignerCompartment> parseXmlCompartmentCollection(final Node compartmentsNode)
       throws InvalidXmlSchemaException, CompartmentParserException {
@@ -87,9 +81,8 @@ public class CompartmentCollectionXmlParser {
 
   /**
    * Creates CellDesigner xml string from set of compartments.
-   * 
-   * @param collection
-   *          collection of compartments to be transformed into xml
+   *
+   * @param collection collection of compartments to be transformed into xml
    * @return xml representation of the compartments
    */
   public String toXml(final Collection<Compartment> collection) {
@@ -104,6 +97,7 @@ public class CompartmentCollectionXmlParser {
       }
     }
     Compartment defaultCompartment = new Compartment("default");
+    defaultCompartment.setName("default");
     result.append(compartmentParser.toXml(defaultCompartment));
     result.append("</listOfCompartments>\n");
     return result.toString();

service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java

@@ -86,7 +86,7 @@ public class SearchService implements ISearchService {
     this.elementDao = elementDao;
     this.reactionDao = reactionDao;
     addSearchPrefix("complex", Collections.singletonList(Complex.class));
-    addSearchPrefix("degrded", Collections.singletonList(Degraded.class));
+    addSearchPrefix("degraded", Collections.singletonList(Degraded.class));
     addSearchPrefix("drug", Collections.singletonList(Drug.class));
     addSearchPrefix("gene", Collections.singletonList(Gene.class));
     addSearchPrefix("ion", Collections.singletonList(Ion.class));