Refactor CoExpressionService to work with iterator over MolecularAlteration objects.

persistence/persistence-api/src/main/java/org/cbioportal/persistence/MolecularDataRepository.java

@@ -14,6 +14,9 @@ public interface MolecularDataRepository {
     List<GeneMolecularAlteration> getGeneMolecularAlterations(String molecularProfileId, List<Integer> entrezGeneIds,
                                                               String projection);
 
+    Iterable<GeneMolecularAlteration> getGeneMolecularAlterationsIterable(String molecularProfileId, List<Integer> entrezGeneIds,
+                                                                          String projection);
+
     List<GeneMolecularAlteration> getGeneMolecularAlterationsInMultipleMolecularProfiles(List<String> molecularProfileIds, 
                                                                                          List<Integer> entrezGeneIds,
                                                                                          String projection);

persistence/persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMapper.java

@@ -4,13 +4,14 @@
 import org.cbioportal.model.GenesetMolecularAlteration;
 
 import java.util.List;
+import org.apache.ibatis.cursor.Cursor;
 
 public interface MolecularDataMapper {
 
     List<String> getCommaSeparatedSampleIdsOfMolecularProfiles(List<String> molecularProfileIds);
 
-    List<GeneMolecularAlteration> getGeneMolecularAlterations(String molecularProfileId, List<Integer> entrezGeneIds,
-                                                              String projection);
+    Cursor<GeneMolecularAlteration> getGeneMolecularAlterations(String molecularProfileId, List<Integer> entrezGeneIds,
+                                                                String projection);
 
     List<GeneMolecularAlteration> getGeneMolecularAlterationsInMultipleMolecularProfiles(List<String> molecularProfileIds, 
                                                                                          List<Integer> entrezGeneIds,

persistence/persistence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepository.java

@@ -4,9 +4,9 @@
 import org.cbioportal.model.GenesetMolecularAlteration;
 import org.cbioportal.persistence.MolecularDataRepository;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.*;
 import org.springframework.stereotype.Repository;
-import java.util.Arrays;
-import java.util.List;
+import java.util.*;
 
 @Repository
 public class MolecularDataMyBatisRepository implements MolecularDataRepository {
@@ -27,9 +27,27 @@ public List<String> getCommaSeparatedSampleIdsOfMolecularProfiles(List<String> m
     }
 
     @Override
+    // cursor processing requires a transaction 
+    @Transactional(readOnly=true, propagation=Propagation.NESTED)
     public List<GeneMolecularAlteration> getGeneMolecularAlterations(String molecularProfileId, 
                                                                      List<Integer> entrezGeneIds, String projection) {
 
+        List<GeneMolecularAlteration> toReturn = new ArrayList();
+        Iterable<GeneMolecularAlteration> gmasItr =
+            molecularDataMapper.getGeneMolecularAlterations(molecularProfileId, entrezGeneIds, projection);
+        for (GeneMolecularAlteration gma : gmasItr) {
+            toReturn.add(gma);
+        }
+        return toReturn;
+    }
+
+    @Override
+    // In order to return a cursor/iterator to the service layer, we need a transaction setup in the service
+    // layer. Currently, the bottom stackframe is CoExpressionService:getCoExpressions.  It is there where
+    // you will find the transaction created.
+    public Iterable<GeneMolecularAlteration> getGeneMolecularAlterationsIterable(String molecularProfileId, 
+                                                                                 List<Integer> entrezGeneIds, String projection) {
+
         return molecularDataMapper.getGeneMolecularAlterations(molecularProfileId, entrezGeneIds, projection);
     }
 

persistence/persistence-mybatis/src/test/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java

@@ -7,6 +7,7 @@
 import org.junit.runner.RunWith;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Configurable;
+import org.springframework.transaction.annotation.Transactional;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 
@@ -43,6 +44,7 @@ public void getCommaSeparatedSampleIdsOfMolecularProfiles() throws Exception {
     }
 
     @Test
+    @Transactional(readOnly=true)
     public void getGeneMolecularAlterations() throws Exception {
 
         List<Integer> entrezGeneIds = new ArrayList<>();

service/src/main/java/org/cbioportal/service/MolecularDataService.java

@@ -23,8 +23,8 @@ List<GeneMolecularData> fetchMolecularData(String molecularProfileId, List<Strin
     BaseMeta fetchMetaMolecularData(String molecularProfileId, List<String> sampleIds, List<Integer> entrezGeneIds) 
         throws MolecularProfileNotFoundException;
 
-    List<GeneMolecularAlteration> getMolecularAlterations(String molecularProfileId, List<Integer> entrezGeneIds, 
-        String projection) throws MolecularProfileNotFoundException;
+   Iterable<GeneMolecularAlteration> getMolecularAlterations(String molecularProfileId, List<Integer> entrezGeneIds, 
+                                                              String projection) throws MolecularProfileNotFoundException;
 
     Integer getNumberOfSamplesInMolecularProfile(String molecularProfileId);