Merge branch '1607-remove-issue' into 'devel_16.0.x'

Resolve "removing project unsuccessful- status failure"

See merge request !1401

CHANGELOG

@@ -5,6 +5,10 @@ minerva (16.0.5) stable; urgency=medium
     consuming (#1605)
   * Bug fix (performance): showing data overlay on big map was time consuming
   * Bug fix: invalid SBML file could crash map upload/format conversion (#1611)
+  * Bug fix: some old maps could not be removed (#1607)
+  * Bug fix: concurency issue when exporting to CellDesigner - minerva could
+    crash when there were two exports running in parallel (#1598)
+  
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 13 Dec 2021 15:00:00 +0200
 

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

@@ -4,13 +4,20 @@ import java.awt.Color;
 import java.awt.geom.Dimension2D;
 import java.awt.geom.Point2D;
 import java.io.ByteArrayInputStream;
-import java.util.*;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
 
-import javax.xml.parsers.*;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
 
 import org.apache.commons.lang3.StringUtils;
 import org.w3c.dom.Node;
-import org.xml.sax.*;
+import org.xml.sax.ErrorHandler;
+import org.xml.sax.SAXException;
+import org.xml.sax.SAXParseException;
 
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidStateException;
@@ -42,23 +49,24 @@ public class CommonXmlParser {
     }
 
     @Override
-    public void setSize(double width, double height) {
+    public void setSize(final double width, final double height) {
       this.width = width;
       this.height = height;
     }
 
   }
 
-  public static Set<MiriamRelationType> RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER;
-  {
-    RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER = new HashSet<>();
-    RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER.addAll(Arrays.asList(MiriamRelationType.values()));
-    RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER.remove(MiriamRelationType.BQ_MODEL_IS_DERIVED_FROM);
-    RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER.remove(MiriamRelationType.BQ_BIOL_HAS_PROPERTY);
-    RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER.remove(MiriamRelationType.BQ_BIOL_IS_PROPERTY_OF);
-    RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER.remove(MiriamRelationType.BQ_MODEL_IS_INSTANCE_OF);
-    RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER.remove(MiriamRelationType.BQ_MODEL_HAS_INSTANCE);
-    RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER.remove(MiriamRelationType.BQ_BIOL_HAS_TAXON);
+  public static final Set<MiriamRelationType> RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER;
+  static {
+    Set<MiriamRelationType> types = new HashSet<>();
+    types.addAll(Arrays.asList(MiriamRelationType.values()));
+    types.remove(MiriamRelationType.BQ_MODEL_IS_DERIVED_FROM);
+    types.remove(MiriamRelationType.BQ_BIOL_HAS_PROPERTY);
+    types.remove(MiriamRelationType.BQ_BIOL_IS_PROPERTY_OF);
+    types.remove(MiriamRelationType.BQ_MODEL_IS_INSTANCE_OF);
+    types.remove(MiriamRelationType.BQ_MODEL_HAS_INSTANCE);
+    types.remove(MiriamRelationType.BQ_BIOL_HAS_TAXON);
+    RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER = Collections.unmodifiableSet(types);
   }
 
   private DocumentBuilderFactory dbFactory;
@@ -70,17 +78,17 @@ public class CommonXmlParser {
       dBuilder = dbFactory.newDocumentBuilder();
       dBuilder.setErrorHandler(new ErrorHandler() {
         @Override
-        public void warning(SAXParseException e) throws SAXException {
+        public void warning(final SAXParseException e) throws SAXException {
           ;
         }
 
         @Override
-        public void fatalError(SAXParseException e) throws SAXException {
+        public void fatalError(final SAXParseException e) throws SAXException {
           throw e;
         }
 
         @Override
-        public void error(SAXParseException e) throws SAXException {
+        public void error(final SAXParseException e) throws SAXException {
           throw e;
         }
       });
@@ -97,7 +105,7 @@ public class CommonXmlParser {
    *          xml node to parse
    * @return Point2D object
    */
-  public Point2D getPosition(Node node) {
+  public Point2D getPosition(final Node node) {
     double x = Double.parseDouble(XmlParser.getNodeAttr("x", node));
     double y = Double.parseDouble(XmlParser.getNodeAttr("y", node));
     return new Point2D.Double(x, y);
@@ -111,7 +119,7 @@ public class CommonXmlParser {
    *          xml node to parse
    * @return dimension (with width and height fields)
    */
-  public Dimension2D getDimension(Node node) {
+  public Dimension2D getDimension(final Node node) {
     double width = Double.parseDouble(XmlParser.getNodeAttr("width", node));
     double height = Double.parseDouble(XmlParser.getNodeAttr("height", node));
     DimensionDouble result = new DimensionDouble();
@@ -126,7 +134,7 @@ public class CommonXmlParser {
    *          xml node to parse
    * @return single line object (with width field)
    */
-  public SingleLine getSingleLine(Node node) {
+  public SingleLine getSingleLine(final Node node) {
     SingleLine result = new SingleLine();
     result.setWidth(Double.parseDouble(XmlParser.getNodeAttr("width", node)));
     return result;
@@ -139,9 +147,10 @@ public class CommonXmlParser {
    *          xml node to parse
    * @return Color value stored in xml
    */
-  public Color getColor(Node node) {
+  public Color getColor(final Node node) {
     String color = XmlParser.getNodeAttr("color", node);
-    // cellDesigner has a bug that removes info about alpha when alpha is 0 (#1103)
+    // cellDesigner has a bug that removes info about alpha when alpha is 0
+    // (#1103)
     color = StringUtils.leftPad(color, 8, "0");
 
     return XmlParser.stringToColor(color);
@@ -155,7 +164,7 @@ public class CommonXmlParser {
    * @return view parsed from xml
    * @see View
    */
-  public View getView(Node node) {
+  public View getView(final Node node) {
     View result = new View();
     Node tmpNode = XmlParser.getNode("celldesigner:innerPosition", node.getChildNodes());
     if (tmpNode != null) {

persist/src/main/resources/db/migration/hsql/16.0.5/V16.0.5.20211215.2__invalid_modification_residue.sql

+update modification_residue_table set modification_type='MODIFICATION_SITE' where modification_type ='';

persist/src/main/resources/db/migration/postgres/16.0.5/V16.0.5.20211215.2__invalid_modification_residue.sql

+update modification_residue_table set modification_type='MODIFICATION_SITE' where modification_type ='';