fetching information about publication with invalid (non numeric) pubmed id triggered exception

CHANGELOG

 minerva (12.2.0~beta.3) unstable; urgency=medium
   * Bug fix: Icons are still not properly loaded on Safari (#661)
+  * Bug fix: fetching information about publication with invalid (non numeric)
+    pubmed id triggered exception (#737)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 6 Mar 2019 17:00:00 +0200
 
 minerva (12.2.0~beta.2) unstable; urgency=medium
   * Bug fix: order of the overlays is defined explicitly also for general 

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java

@@ -11,6 +11,7 @@ import java.util.Set;
 import java.util.SortedMap;
 import java.util.TreeMap;
 
+import org.apache.commons.lang3.math.NumberUtils;
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
@@ -21,6 +22,7 @@ import lcsb.mapviewer.annotation.services.PubmedParser;
 import lcsb.mapviewer.annotation.services.PubmedSearchException;
 import lcsb.mapviewer.api.BaseRestImpl;
 import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.comparator.IntegerComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
@@ -89,7 +91,7 @@ public class PublicationsRestImpl extends BaseRestImpl {
     this.searchService = searchService;
   }
 
-  private enum SortColumn {
+  enum SortColumn {
     PUBMED_ID("pubmedId"),
     YEAR("year"),
     JOURNAL("journal"),
@@ -122,8 +124,8 @@ public class PublicationsRestImpl extends BaseRestImpl {
     List<Map.Entry<MiriamData, List<BioEntity>>> filteredList = new ArrayList<>();
 
     for (Map.Entry<MiriamData, List<BioEntity>> entry : publications.entrySet()) {
-      Set<Model> publicationModels= new HashSet<>();
-      for (BioEntity bioEntity: entry.getValue()) {
+      Set<Model> publicationModels = new HashSet<>();
+      for (BioEntity bioEntity : entry.getValue()) {
         publicationModels.add(bioEntity.getModel());
       }
       if (isSearchResult(entry.getKey(), search, publicationModels)) {
@@ -159,7 +161,7 @@ public class PublicationsRestImpl extends BaseRestImpl {
     return result;
   }
 
-  private Comparator<Entry<MiriamData, List<BioEntity>>> getComparatorForColumn(SortColumn sortColumnEnum,
+  Comparator<Entry<MiriamData, List<BioEntity>>> getComparatorForColumn(SortColumn sortColumnEnum,
       String sortOrder) {
     final int orderFactor;
     if (sortOrder.toLowerCase().equals("desc")) {
@@ -171,13 +173,16 @@ public class PublicationsRestImpl extends BaseRestImpl {
       return null;
     } else if (sortColumnEnum.equals(SortColumn.PUBMED_ID)) {
       return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
+        IntegerComparator integerComparator = new IntegerComparator();
+
         @Override
         public int compare(Entry<MiriamData, List<BioEntity>> o1, Entry<MiriamData, List<BioEntity>> o2) {
-          Integer id1 = Integer.valueOf(o1.getKey().getResource());
-          Integer id2 = Integer.valueOf(o2.getKey().getResource());
-          return id1.compareTo(id2) * orderFactor;
+          Integer id1 = extractPubmedId(o1.getKey());
+          Integer id2 = extractPubmedId(o2.getKey());
+          return integerComparator.compare(id1, id2) * orderFactor;
 
         }
+
       };
     } else if (sortColumnEnum.equals(SortColumn.YEAR)) {
       return new Comparator<Map.Entry<MiriamData, List<BioEntity>>>() {
@@ -310,4 +315,13 @@ public class PublicationsRestImpl extends BaseRestImpl {
     return pubmedParser.getPubmedArticleById(Integer.valueOf(resource));
   }
 
+  private Integer extractPubmedId(MiriamData md) {
+    if (NumberUtils.isDigits(md.getResource())) {
+      return Integer.valueOf(md.getResource());
+    } else {
+      return null;
+    }
+
+  }
+
 }

rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java

 package lcsb.mapviewer.api.projects.models.publications;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
 
+import java.util.ArrayList;
+import java.util.Comparator;
 import java.util.List;
 import java.util.Map;
+import java.util.TreeMap;
+import java.util.Map.Entry;
 
 import org.apache.log4j.Logger;
 import org.junit.After;
@@ -19,6 +24,10 @@ import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.api.QueryException;
 import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.api.projects.models.publications.PublicationsRestImpl.SortColumn;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.services.interfaces.IModelService;
 
@@ -124,4 +133,48 @@ public class PublicationsRestImplTest extends RestTestFunctions {
     return _projectRestImpl;
   }
 
+  @Test
+  public void testComparatorForColumnWithInvalidData() {
+    Entry<MiriamData, List<BioEntity>> valid = new Entry<MiriamData, List<BioEntity>>() {
+      
+      @Override
+      public List<BioEntity> setValue(List<BioEntity> value) {
+        return null;
+      }
+      
+      @Override
+      public List<BioEntity> getValue() {
+        return new ArrayList<>();
+      }
+      
+      @Override
+      public MiriamData getKey() {
+        return new MiriamData(MiriamType.PUBMED, "12345");
+      }
+    };
+    Entry<MiriamData, List<BioEntity>> invalid = new Entry<MiriamData, List<BioEntity>>() {
+      
+      @Override
+      public List<BioEntity> setValue(List<BioEntity> value) {
+        return null;
+      }
+      
+      @Override
+      public List<BioEntity> getValue() {
+        return new ArrayList<>();
+      }
+      
+      @Override
+      public MiriamData getKey() {
+        return new MiriamData(MiriamType.PUBMED, "");
+      }
+    };
+    for (SortColumn sortColumn : SortColumn.values()) {
+      Comparator<Entry<MiriamData, List<BioEntity>>> comparator = _projectRestImpl.getComparatorForColumn(sortColumn,
+          "desc");
+      assertNotNull(comparator.compare(valid, invalid));
+      
+    }
+  }
+
 }