Merge branch '1140-corrupted-drug-db' into 'devel_14.0.x'

when there is problem with deserialization carry on without throwing error

See merge request minerva/core!1072

CHANGELOG

@@ -23,8 +23,9 @@ minerva (14.0.9) stable; urgency=medium
   * Bug fix: reaction without product in SBGN crashed upload of map
   * Bug fix: when SBGN production pointed directly to process instead of
     process port upload crashed
+  * Bug fix: handle properly corrupted cached chembl drug data (#1140)
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 3 Feb 2020 15:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 25 Feb 2020 15:00:00 +0200
 
 minerva (14.0.8) stable; urgency=medium
   * Bug fix: API didn't allow to upload pluins with local url (#1084,

annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java

@@ -4,6 +4,7 @@ import java.io.IOException;
 import java.net.URLEncoder;
 import java.util.*;
 
+import org.apache.commons.lang3.SerializationException;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -319,9 +320,13 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
 
     String query = NAME_PREFIX + name.toLowerCase().trim();
 
-    Drug drug = getDrugSerializer().xmlToObject(getCacheNode(query));
-    if (drug != null) {
-      return drug;
+    try {
+      Drug drug = getDrugSerializer().xmlToObject(getCacheNode(query));
+      if (drug != null) {
+        return drug;
+      }
+    } catch (SerializationException e) {
+      logger.error(e, e);
     }
 
     try {
@@ -331,13 +336,13 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
 
       Document document = XmlParser.getXmlDocumentFromString(page);
       List<Drug> drugs = extractDrugsFromDocument(document);
-      if (drugs.size()==0) {
+      if (drugs.size() == 0) {
         accessUrl = DRUG_SYNONYM_API_URL + name;
         page = getWebPageContent(accessUrl);
         document = XmlParser.getXmlDocumentFromString(page);
         drugs = extractDrugsFromDocument(document);
       }
-      if (drugs.size()>1) {
+      if (drugs.size() > 1) {
         logger.warn("More drugs than one found for query: " + query);
       }
 

annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java

@@ -7,10 +7,13 @@ import static org.mockito.Mockito.when;
 import java.io.IOException;
 import java.util.*;
 
+import org.apache.commons.lang3.SerializationException;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.junit.Test;
 import org.mockito.Mockito;
+import org.mockito.invocation.InvocationOnMock;
+import org.mockito.stubbing.Answer;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.w3c.dom.Node;
 
@@ -889,4 +892,22 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testFindDrugWhenSerializerFails() throws Exception {
+    ChEMBLParser parser = Mockito.spy(chemblParser);
+
+    when(parser.getDrugSerializer()).then(new Answer<XmlSerializer<Drug>>() {
+
+      @Override
+      public XmlSerializer<Drug> answer(InvocationOnMock invocation) throws Throwable {
+        @SuppressWarnings("unchecked")
+        XmlSerializer<Drug> serializer = Mockito.mock(XmlSerializer.class);
+        when(serializer.xmlToObject(any())).thenThrow(new SerializationException());
+        return serializer;
+      }
+    });
+
+    assertNotNull(parser.findDrug("CABOZANTINIB"));
+  }
+
 }