Merge branch '785-entrez' into 'devel_12.2.x'

Resolve "annotating protein created model that cannot be exported properly"

See merge request minerva/core!729

CHANGELOG

@@ -10,6 +10,8 @@ minerva (12.2.2) stable; urgency=medium
   * Bug fix: removing project without full control in the system (but with 
     enough privileges to remove project) caused "Not enough privileges" error 
     (#778)
+  * Bug fix: export of custom properties (like synonyms) are properly encoded 
+    in CellDesigner xml (#785)
 
 minerva (12.2.1) stable; urgency=medium
   * Bug fix: export of reaction colorsi in SBML is properly encoded (COPASI can

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java

 package lcsb.mapviewer.annotation.services.annotators;
 
 import java.io.IOException;
-import java.io.StringReader;
 import java.net.HttpURLConnection;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -9,15 +8,11 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
+import org.apache.commons.text.StringEscapeUtils;
 import org.apache.log4j.Logger;
 import org.springframework.stereotype.Service;
-import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
 
 import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
 import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
@@ -300,7 +295,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
 						Node node = list.item(i);
 						if (node.getNodeType() == Node.ELEMENT_NODE) {
 							if (node.getNodeName().equals("Gene-ref_syn_E")) {
-								synonyms.add(node.getTextContent());
+								synonyms.add(StringEscapeUtils.unescapeHtml4(node.getTextContent()));
 							}
 						}
 					}

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java

@@ -343,6 +343,23 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testAnnotateElementWithEncodedSynonyms() throws Exception {
+    try {
+      Species proteinAlias = new GenericProtein("id");
+      proteinAlias.addMiriamData(new MiriamData(MiriamType.ENTREZ, "834106"));
+      entrezAnnotator.annotateElement(proteinAlias);
+
+      for (String synonym : proteinAlias.getSynonyms()) {
+        assertFalse("Invalid character found in synonym: " + synonym, synonym.contains("&"));
+      }
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testParseEntrezResponse() throws Exception {
     WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();

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

@@ -160,8 +160,9 @@ public class RestAnnotationParser extends XmlParser {
         return "";
       }
     } else if (value instanceof String) {
-      if (!((String) value).trim().isEmpty() || forceFullInfo) {
-        return type.getCommonName() + ": " + value + "\n";
+      String string =(String) value; 
+      if (!(string.trim().isEmpty()) || forceFullInfo) {
+        return type.getCommonName() + ": " + super.escapeXml(string) + "\n";
       } else {
         return "";
       }
@@ -178,7 +179,7 @@ public class RestAnnotationParser extends XmlParser {
           if (object instanceof MiriamData) {
             result += ((MiriamData) object).getResource();
           } else {
-            result += object;
+            result += super.escapeXml(object.toString());
           }
 
         }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java

@@ -54,6 +54,8 @@ import lcsb.mapviewer.model.map.species.Species;
 public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
   Logger logger = Logger.getLogger(CellDesignerXmlParserTest.class);
 
+  ModelComparator modelComparator = new ModelComparator();
+
   @Before
   public void setUp() throws Exception {
   }
@@ -422,8 +424,6 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
       InputStream is = new ByteArrayInputStream(xmlString.getBytes());
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
-      ModelComparator modelComparator = new ModelComparator();
-
       assertEquals(0, modelComparator.compare(model, model2));
 
     } catch (Exception e) {
@@ -1012,6 +1012,34 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
     }
   }
 
+  @Test
+  public void testSpeciesWithSpecialSynonym() throws Exception {
+    try {
+      Model model = new ModelFullIndexed(null);
+      model.setIdModel("as");
+      model.setWidth(10);
+      model.setHeight(10);
+      Species protein = new GenericProtein("id1");
+      protein.setWidth(10);
+      protein.setHeight(10);
+      protein.setName("ROS");
+      protein.addSynonym("&");
+      model.addElement(protein);
+
+      CellDesignerXmlParser parser = new CellDesignerXmlParser();
+      String xmlString = parser.toXml(model);
+      InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+
+      Model model2 = parser.createModel(new ConverterParams().inputStream(is));
+      
+      assertEquals(0, modelComparator.compare(model, model2));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testReactionCoordsEqual() throws Exception {
     try {