Merge branch '764-invalid-pubmed-id' into 'devel_12.2.x'

invalid pubmed id could break clicking on elements or listing publications

See merge request !721

CHANGELOG

@@ -4,6 +4,8 @@ minerva (12.2.1) stable; urgency=medium
   * Bug fix: removing active plugin didn't switch plugin tab to the next loaded 
     plugin (#757)
   * Bug fix: closed submap will not be reopened after page refresh (#763) 
+  * Bug fix: invalid pubmed identifier could break clicking on element 
+    containing it (#764, #765, #769)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 1 Apr 2019 17:00:00 +0200
 

rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java

@@ -19,6 +19,7 @@ import javax.xml.transform.TransformerFactoryConfigurationError;
 import javax.xml.transform.stream.StreamResult;
 import javax.xml.transform.stream.StreamSource;
 
+import org.apache.commons.lang3.math.NumberUtils;
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.io.ClassPathResource;
@@ -116,11 +117,15 @@ public abstract class BaseRestImpl {
         }
       }
       if (MiriamType.PUBMED.equals(annotation.getDataType())) {
-        try {
-          Article article = pubmedParser.getPubmedArticleById(annotation.getResource());
-          result.put("article", article);
-        } catch (PubmedSearchException e) {
-          logger.error("Problem with accessing info about pubmed", e);
+        if (NumberUtils.isDigits(annotation.getResource())) {
+          try {
+            Article article = pubmedParser.getPubmedArticleById(annotation.getResource());
+            result.put("article", article);
+          } catch (PubmedSearchException e) {
+            logger.error("Problem with accessing info about pubmed", e);
+          }
+        } else {
+          logger.error("Invalid pubmed identifier: " + annotation.getResource());
         }
       }
       result.put("type", annotation.getDataType().name());

rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java

@@ -20,10 +20,10 @@ import lcsb.mapviewer.model.map.MiriamType;
 
 public class BaseRestImplTest extends RestTestFunctions {
   Logger logger = Logger.getLogger(BaseRestImplTest.class);
-  
+
   @Autowired
   MiriamConnector mc;
-  
+
   @Autowired
   PubmedParser pubmedParser;
 
@@ -44,7 +44,7 @@ public class BaseRestImplTest extends RestTestFunctions {
     String presentationXml2 = controller.mathMLToPresentationML(content);
     assertEquals(presentationXml, presentationXml2);
   }
-  
+
   @Test
   public void testMathMLToPresentationMLCalledTwiceShouldntHaveXmlNode() throws Exception {
     BaseRestImpl controller = Mockito.mock(BaseRestImpl.class, CALLS_REAL_METHODS);
@@ -52,16 +52,31 @@ public class BaseRestImplTest extends RestTestFunctions {
     String presentationXml = controller.mathMLToPresentationML(content);
     assertFalse(presentationXml.startsWith("<?xml"));
   }
-  
+
   @Test
   public void testCreateAnnotationWithWhitespace() throws Exception {
     BaseRestImpl controller = Mockito.mock(BaseRestImpl.class, CALLS_REAL_METHODS);
     controller.setMiriamConnector(mc);
     controller.setPubmedParser(pubmedParser);
-    Map<String, Object> response = controller.createAnnotation(new MiriamData(MiriamType.PUBMED,"28255955 "));
+    Map<String, Object> response = controller.createAnnotation(new MiriamData(MiriamType.PUBMED, "28255955 "));
     assertNotNull(response);
   }
-  
-  
 
+  @Test
+  public void testCreateAnnotationWithNonNumericValues() throws Exception {
+    BaseRestImpl controller = Mockito.mock(BaseRestImpl.class, CALLS_REAL_METHODS);
+    controller.setMiriamConnector(mc);
+    controller.setPubmedParser(pubmedParser);
+    Map<String, Object> response = controller.createAnnotation(new MiriamData(MiriamType.PUBMED, "28255955PG"));
+    assertNotNull(response);
+  }
+
+  @Test
+  public void testCreateAnnotationWithEmptyValue() throws Exception {
+    BaseRestImpl controller = Mockito.mock(BaseRestImpl.class, CALLS_REAL_METHODS);
+    controller.setMiriamConnector(mc);
+    controller.setPubmedParser(pubmedParser);
+    Map<String, Object> response = controller.createAnnotation(new MiriamData(MiriamType.PUBMED, ""));
+    assertNotNull(response);
+  }
 }