From 495c777c89496fed9c0b078cd6c25cd9c9b8412c Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Wed, 19 Feb 2025 14:01:12 +0100
Subject: [PATCH] add name when exporting default compartment
---
CHANGELOG | 3 +-
.../CompartmentCollectionXmlParser.java | 54 +++++++++----------
2 files changed, 26 insertions(+), 31 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 79d73f90e0..86075ff0b1 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,8 +1,9 @@
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
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
index 1cfef66dd4..228410c4d3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java
@@ -1,16 +1,5 @@
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();
--
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