search by target didn't work if target was annotated automatically

CHANGELOG

@@ -22,6 +22,8 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
     with SBML standard (#831)
   * Bug fix: MiRNA targets are limited only to the organism associated with the 
     map (#66)
+  * Bug fix: Search drug by target element did not return values when this 
+    element was annotated automatically (#216)
 
  -- Sascha Herzinger <sascha.herzinger@uni.lu>  Wed, 22 May 2019 10:30:00 +0200
 

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

@@ -621,12 +621,13 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
   }
 
   @Override
-  public List<Drug> getDrugListByTarget(MiriamData targetMiriamData, Collection<MiriamData> organisms)
+  public List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms)
       throws DrugSearchException {
     List<Drug> result = new ArrayList<>();
-    if (targetMiriamData == null) {
+    if (target == null) {
       return result;
     }
+    MiriamData targetMiriamData = new MiriamData(target.getDataType(), target.getResource());
     if (!(MiriamType.HGNC_SYMBOL.equals(targetMiriamData.getDataType()))) {
       throw new InvalidArgumentException("Only " + MiriamType.HGNC_SYMBOL + " type is accepted");
     }
@@ -747,10 +748,13 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
    * the target and we need to filter it out (here is an example for TF targets:
    * https://www.drugbank.ca/unearth/q?utf8=%E2%9C%93&searcher=targets&query=TF)
    *
-   * @param page - target webpage content
-   * @param hgncTarget - HGNC identifier that should match the target
+   * @param page
+   *          - target webpage content
+   * @param hgncTarget
+   *          - HGNC identifier that should match the target
    * @return
-   * @throws UniprotSearchException - when there is problem with translating HGNC<->uniprot
+   * @throws UniprotSearchException
+   *           - when there is problem with translating HGNC<->uniprot
    */
   boolean targetPageMatchTarget(String page, MiriamData hgncTarget) throws UniprotSearchException {
     int protienLinkPosition = page.indexOf("/polypeptides/");

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

@@ -470,8 +470,8 @@ public class MiRNAParser extends CachableInterface implements IExternalService {
    * the parameter.
    * 
    * @param targetsMiriam
-   *          targets that should be targeted by resulting mir rnas
-   * @return list of mirnas that target elements identified by paramter
+   *          targets that should be targeted by resulting mirnas
+   * @return list of mirnas that target elements identified by parameter
    * @throws MiRNASearchException
    *           thrown when there is a problem with accessing mirna database
    */

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

@@ -273,6 +273,23 @@ public class ChemicalParserTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testGetByTargetWithAnnotator() throws Exception {
+    try {
+      MiriamData target = new MiriamData(MiriamType.HGNC_SYMBOL, "GCH1", String.class);
+      List<MiriamData> targets = new ArrayList<>();
+      targets.add(target);
+
+      List<Chemical> list = chemicalParser.getChemicalListByTarget(targets, dystoniaDisease);
+      assertNotNull(list);
+      assertFalse(list.isEmpty());
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testGetByInvalidTarget() throws Exception {
     try {

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

@@ -238,6 +238,19 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testFindDrugByHgncTargetWithAnnotatorAssigned() throws Exception {
+    try {
+      List<Drug> drugs = drugBankHTMLParser.getDrugListByTarget(new MiriamData(MiriamType.HGNC_SYMBOL, "SIRT3", String.class));
+      assertNotNull(drugs);
+      assertTrue("At least 1 drug was expected", drugs.size() >= 1);
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testTargetPageMatchTargetForTFProtein() throws Exception {
     try {

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

@@ -159,6 +159,31 @@ public class MiRNAParserTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testFindByTargetWithAnnotator() throws Exception {
+
+    try {
+      Set<MiriamData> targets = new HashSet<>();
+      MiriamData hgncTarget = new MiriamData(MiriamType.HGNC_SYMBOL, "PLAG1", String.class);
+      targets.add(hgncTarget);
+      List<MiRNA> listFromDB = miRNAParser.getMiRnaListByTargets(targets);
+      assertTrue(listFromDB.size() > 0);
+      hgncTarget.setAnnotator(null);
+      for (MiRNA miRNA : listFromDB) {
+        boolean found = false;
+        for (Target targt : miRNA.getTargets()) {
+          if (targt.getGenes().contains(hgncTarget)) {
+            found = true;
+          }
+        }
+        assertTrue(found);
+      }
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test(timeout = 50000)
   public void testCachableInterfaceInvalidateMiRNA() throws Exception {
     try {