mirna targets are filtered by organism

CHANGELOG

@@ -18,6 +18,8 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
     inside boolean gateway
   * Bug fix: CellDesigner file exported from minerva was not fully compliant
     with SBML standard (#831)
+  * Bug fix: MiRNA targets are limited only to the organism associated with the 
+    map (#66)
 
  -- Sascha Herzinger <sascha.herzinger@uni.lu>  Wed, 22 May 2019 10:30:00 +0200
 

service/src/main/java/lcsb/mapviewer/services/search/mirna/MiRNAService.java

@@ -7,7 +7,8 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
@@ -71,6 +72,7 @@ public class MiRNAService extends DbSearchService implements IMiRNAService {
       names.add(name);
       List<MiRNA> miRNAs = miRNAParser.getMiRnasByNames(names);
       if (miRNAs.size() > 0) {
+        removeUnknownOrganisms(miRNAs.get(0), searchCriteria.getOrganisms());
         return miRNAs.get(0);
       }
       return null;
@@ -117,8 +119,8 @@ public class MiRNAService extends DbSearchService implements IMiRNAService {
       logger.error("Problem with accessing mirna database", e);
     }
 
-    for (MiRNA drug : mirnaList) {
-      removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
+    for (MiRNA mirna : mirnaList) {
+      removeUnknownOrganisms(mirna, searchCriteria.getOrganisms());
     }
 
     Collections.sort(mirnaList, new MiRNA.NameComparator());
@@ -128,15 +130,15 @@ public class MiRNAService extends DbSearchService implements IMiRNAService {
   /**
    * Removes targets for unknown organisms from the mirna.
    * 
-   * @param drug
-   *          drug from which we want to remove targets
+   * @param mirna
+   *          mirna from which we want to remove targets
    * @param organisms
    *          organisms that should be kept
    */
-  private void removeUnknownOrganisms(MiRNA drug, List<MiriamData> organisms) {
+  private void removeUnknownOrganisms(MiRNA mirna, List<MiriamData> organisms) {
     if (organisms.size() > 0) {
       List<Target> toRemove = new ArrayList<Target>();
-      for (Target target : drug.getTargets()) {
+      for (Target target : mirna.getTargets()) {
         boolean remove = true;
         for (MiriamData organism : organisms) {
           if (target.getOrganism() == null) {
@@ -151,7 +153,7 @@ public class MiRNAService extends DbSearchService implements IMiRNAService {
           toRemove.add(target);
         }
       }
-      drug.getTargets().removeAll(toRemove);
+      mirna.getTargets().removeAll(toRemove);
     }
   }
 

service/src/test/java/lcsb/mapviewer/services/search/mirna/MiRNAServiceTest.java

 package lcsb.mapviewer.services.search.mirna;
 
-import org.apache.logging.log4j.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
 
+import lcsb.mapviewer.annotation.data.MiRNA;
+import lcsb.mapviewer.annotation.data.Target;
+import lcsb.mapviewer.annotation.services.TaxonomyBackend;
 import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.search.mirna.IMiRNAService;
+import lcsb.mapviewer.services.search.DbSearchCriteria;
 
 public class MiRNAServiceTest extends ServiceTestFunctions {
   Logger logger = LogManager.getLogger(MiRNAServiceTest.class);
@@ -45,4 +54,22 @@ public class MiRNAServiceTest extends ServiceTestFunctions {
     }
   }
 
+  @Test
+  public void testFindMiRNAFilteredByOrganism() throws Exception {
+    try {
+      MiRNA test = miRNAService.getByName("hsa-miR-29a-3p",
+          new DbSearchCriteria().organisms(TaxonomyBackend.HUMAN_TAXONOMY));
+      assertNotNull(test);
+      for (Target t : test.getTargets()) {
+        for (MiriamData md : t.getGenes()) {
+          assertEquals("Only hgnc symbols should be used for gene annotations", MiriamType.HGNC_SYMBOL,
+              md.getDataType());
+        }
+      }
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
 }