Reintroduction of Cursor code to optimzation memory usage of CoExpres…

…sion service.

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

@@ -20,6 +20,10 @@ public interface MolecularDataRepository {
     List<GeneMolecularAlteration> getGeneMolecularAlterations(String molecularProfileId, List<Integer> entrezGeneIds,
                                                               String projection);
 
+    @Cacheable(cacheNames = "GeneralRepositoryCache", condition = "@cacheEnabledConfig.getEnabled()")
+    Iterable<GeneMolecularAlteration> getGeneMolecularAlterationsIterable(String molecularProfileId, List<Integer> entrezGeneIds,
+                                                                          String projection);
+
     @Cacheable(cacheNames = "GeneralRepositoryCache", condition = "@cacheEnabledConfig.getEnabled()")
     List<GeneMolecularAlteration> getGeneMolecularAlterationsInMultipleMolecularProfiles(List<String> molecularProfileIds,
                                                                                          List<Integer> entrezGeneIds,

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

@@ -6,6 +6,7 @@
 import org.cbioportal.model.TreatmentMolecularAlteration;
 
 import java.util.List;
+import org.apache.ibatis.cursor.Cursor;
 
 public interface MolecularDataMapper {
 
@@ -14,6 +15,9 @@ public interface MolecularDataMapper {
     List<GeneMolecularAlteration> getGeneMolecularAlterations(String molecularProfileId, List<Integer> entrezGeneIds,
                                                               String projection);
 
+    Cursor<GeneMolecularAlteration> getGeneMolecularAlterationsIter(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/MolecularDataMyBatisRepository.java

@@ -39,6 +39,16 @@ public List<GeneMolecularAlteration> getGeneMolecularAlterations(String molecula
         return molecularDataMapper.getGeneMolecularAlterations(molecularProfileId, entrezGeneIds, projection);
     }
 
+    @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.getGeneMolecularAlterationsIter(molecularProfileId, entrezGeneIds, projection);
+    }
+
     @Override
     public List<GeneMolecularAlteration> getGeneMolecularAlterationsInMultipleMolecularProfiles(List<String> molecularProfileIds, 
                                                                                                 List<Integer> entrezGeneIds, 

persistence/persistence-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MolecularDataMapper.xml

@@ -63,6 +63,36 @@
         </where>
     </select>
 
+    <!-- This routine is a copy of getGeneMolecularAlterations above.  This copy is necessary because
+         it is backing a corresponding method in MolecularDataMapper.java which returns a Cursor as
+         opposed to a List. This method should be kept in sync with getGeneMolecularAlterations above.
+         (Attempts where made to share getGeneMolecularAlterations between methods in MolecularDataMapper.java
+         all of which have failed).
+    -->
+    <select id="getGeneMolecularAlterationsIter" resultType="org.cbioportal.model.GeneMolecularAlteration">
+        SELECT
+        gene.ENTREZ_GENE_ID AS entrezGeneId,
+        genetic_alteration.VALUES AS "values"
+        <if test="projection == 'DETAILED'">
+            ,
+            <include refid="org.cbioportal.persistence.mybatis.GeneMapper.select">
+                <property name="prefix" value="gene."/>
+            </include>
+        </if>
+        FROM genetic_alteration
+        INNER JOIN genetic_profile ON genetic_alteration.GENETIC_PROFILE_ID = genetic_profile.GENETIC_PROFILE_ID
+        INNER JOIN gene ON genetic_alteration.GENETIC_ENTITY_ID = gene.GENETIC_ENTITY_ID
+        <where>
+            genetic_profile.STABLE_ID = #{molecularProfileId}
+            <if test="entrezGeneIds != null and !entrezGeneIds.isEmpty()">
+                AND gene.ENTREZ_GENE_ID IN
+                <foreach item="item" collection="entrezGeneIds" open="(" separator="," close=")">
+                    #{item}
+                </foreach>
+            </if>
+        </where>
+    </select>
+
     <select id="getGeneMolecularAlterationsInMultipleMolecularProfiles" resultType="org.cbioportal.model.GeneMolecularAlteration">
         SELECT
         gene.ENTREZ_GENE_ID AS entrezGeneId,

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;
 
@@ -18,10 +19,10 @@
 @ContextConfiguration("/testContextDatabase.xml")
 @Configurable
 public class MolecularDataMyBatisRepositoryTest {
-    
+
     @Autowired
     private MolecularDataMyBatisRepository molecularDataMyBatisRepository;
-    
+
     @Test
     public void getCommaSeparatedSampleIdsOfMolecularProfile() throws Exception {
 
@@ -48,20 +49,43 @@ public void getGeneMolecularAlterations() throws Exception {
         List<Integer> entrezGeneIds = new ArrayList<>();
         entrezGeneIds.add(207);
         entrezGeneIds.add(208);
-        
+
         List<GeneMolecularAlteration> result = molecularDataMyBatisRepository.getGeneMolecularAlterations("study_tcga_pub_gistic",
             entrezGeneIds, "SUMMARY");
-
+
+        getGeneMolecularAlterationsCommonTest(result);
+    }
+
+    @Test
+    @Transactional(readOnly=true)
+    public void getGeneMolecularAlterationsIterable() throws Exception {
+
+        List<Integer> entrezGeneIds = new ArrayList<>();
+        entrezGeneIds.add(207);
+        entrezGeneIds.add(208);
+
+        List<GeneMolecularAlteration> result = new ArrayList<>();
+        Iterable<GeneMolecularAlteration> gmaItr = molecularDataMyBatisRepository.getGeneMolecularAlterationsIterable("study_tcga_pub_gistic",
+                                                                                                                      entrezGeneIds, "SUMMARY");
+        for (GeneMolecularAlteration gma : gmaItr) {
+            result.add(gma);
+        }
+
+        getGeneMolecularAlterationsCommonTest(result);
+    }
+
+    private void getGeneMolecularAlterationsCommonTest(List<GeneMolecularAlteration> result) {
+
         Assert.assertEquals(2, result.size());
         GeneMolecularAlteration molecularAlteration1 = result.get(0);
         Assert.assertEquals((Integer) 207, molecularAlteration1.getEntrezGeneId());
         String[] expected = {"-0.4674","-0.6270","-1.2266","-1.2479","-1.2262","0.6962","-0.3338","-0.1264","0.7559","-1.1267","-0.5893",
-        "-1.1546","-1.0027","-1.3157",""};
+                             "-1.1546","-1.0027","-1.3157",""};
         Assert.assertArrayEquals(expected, molecularAlteration1.getSplitValues());
         GeneMolecularAlteration molecularAlteration2 = result.get(1);
         Assert.assertEquals((Integer) 208, molecularAlteration2.getEntrezGeneId());
         String[] expected2 = {"1.4146","-0.0662","-0.8585","-1.6576","-0.3552","-0.8306","0.8102","0.1146","0.3498","0.0349","0.4927",
-                "-0.8665","-0.4754","-0.7221",""};
+                              "-0.8665","-0.4754","-0.7221",""};
         Assert.assertArrayEquals(expected2, molecularAlteration2.getSplitValues());
     }
 
@@ -71,11 +95,11 @@ public void getGeneMolecularAlterationsInMultipleMolecularProfiles() throws Exce
         List<Integer> entrezGeneIds = new ArrayList<>();
         entrezGeneIds.add(207);
         entrezGeneIds.add(208);
-        
+
         List<GeneMolecularAlteration> result = molecularDataMyBatisRepository
             .getGeneMolecularAlterationsInMultipleMolecularProfiles(Arrays.asList("study_tcga_pub_gistic", "study_tcga_pub_mrna"),
             entrezGeneIds, "SUMMARY");
-        
+
         Assert.assertEquals(3, result.size());
         GeneMolecularAlteration molecularAlteration1 = result.get(0);
         Assert.assertEquals((Integer) 207, molecularAlteration1.getEntrezGeneId());

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

@@ -9,27 +9,27 @@
 
 public interface MolecularDataService {
 
-    List<GeneMolecularData> getMolecularData(String molecularProfileId, String sampleListId, 
-                                             List<Integer> entrezGeneIds, String projection) 
+    List<GeneMolecularData> getMolecularData(String molecularProfileId, String sampleListId,
+                                             List<Integer> entrezGeneIds, String projection)
         throws MolecularProfileNotFoundException;
 
-    BaseMeta getMetaMolecularData(String molecularProfileId, String sampleListId, List<Integer> entrezGeneIds) 
+    BaseMeta getMetaMolecularData(String molecularProfileId, String sampleListId, List<Integer> entrezGeneIds)
         throws MolecularProfileNotFoundException;
-    
-    List<GeneMolecularData> fetchMolecularData(String molecularProfileId, List<String> sampleIds, 
-                                               List<Integer> entrezGeneIds, String projection) 
+
+    List<GeneMolecularData> fetchMolecularData(String molecularProfileId, List<String> sampleIds,
+                                               List<Integer> entrezGeneIds, String projection)
         throws MolecularProfileNotFoundException;
 
-    BaseMeta fetchMetaMolecularData(String molecularProfileId, List<String> sampleIds, List<Integer> entrezGeneIds) 
+    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);
 
-    List<GeneMolecularData> getMolecularDataInMultipleMolecularProfiles(List<String> molecularProfileIds, 
-                                                                        List<String> sampleIds, List<Integer> entrezGeneIds, 
+    List<GeneMolecularData> getMolecularDataInMultipleMolecularProfiles(List<String> molecularProfileIds,
+                                                                        List<String> sampleIds, List<Integer> entrezGeneIds,
                                                                         String projection);
 
 	BaseMeta getMetaMolecularDataInMultipleMolecularProfiles(List<String> molecularProfileIds, List<String> sampleIds,