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Reintroduction of Cursor code to optimization memory usage of CoExpression Service #6834

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Nov 22, 2019
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Reintroduction of Cursor code to optimization memory usage of CoExpression Service #6834

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4 changes: 4 additions & 0 deletions ...nce/persistence-api/src/main/java/org/cbioportal/persistence/MolecularDataRepository.java
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Expand Up @@ -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,
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4 changes: 4 additions & 0 deletions ...istence-mybatis/src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMapper.java
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Expand Up @@ -6,6 +6,7 @@
import org.cbioportal.model.TreatmentMolecularAlteration;

import java.util.List;
import org.apache.ibatis.cursor.Cursor;

public interface MolecularDataMapper {

Expand All @@ -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);

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10 changes: 10 additions & 0 deletions ...atis/src/main/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepository.java
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Expand Up @@ -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,
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30 changes: 30 additions & 0 deletions ...nce-mybatis/src/main/resources/org/cbioportal/persistence/mybatis/MolecularDataMapper.xml
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Expand Up @@ -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,
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40 changes: 32 additions & 8 deletions .../src/test/java/org/cbioportal/persistence/mybatis/MolecularDataMyBatisRepositoryTest.java
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Expand Up @@ -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;

Expand All @@ -18,10 +19,10 @@
@ContextConfiguration("/testContextDatabase.xml")
@Configurable
public class MolecularDataMyBatisRepositoryTest {

@Autowired
private MolecularDataMyBatisRepository molecularDataMyBatisRepository;

@Test
public void getCommaSeparatedSampleIdsOfMolecularProfile() throws Exception {

Expand All @@ -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());
}

Expand All @@ -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());
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24 changes: 12 additions & 12 deletions service/src/main/java/org/cbioportal/service/MolecularDataService.java
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Expand Up @@ -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,
Expand Down