Update cBioPortal to dynamically load ch Components only when property clickhouse_enabled is set

.circleci/config.yml

@@ -299,7 +299,7 @@ jobs:
             name: Instantiate a cbioportal instance
             environment:
               DOCKER_REPO: cbioportal/cbioportal-dev
-              CLICKHOUSE_MODE: true
+              APP_CLICKHOUSE_MODE: "true"
             command: |
               cd cbioportal-test
               export DOCKER_IMAGE_CBIOPORTAL=$DOCKER_REPO:$CIRCLE_SHA1-web-shenandoah

.github/workflows/integration-test.yml

@@ -42,9 +42,9 @@ jobs:
         run: |
           cd ./data && ./init.sh && rm -rf ./studies/* && cd ../config && \
           cat $PORTAL_SOURCE_DIR/src/main/resources/application.properties | \
-              sed 's|spring.datasource.mysql.url=.*|spring.datasource.mysql.url=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false|' | \
-              sed 's|spring.datasource.mysql.username=.*|spring.datasource.mysql.username=cbio_user|' | \
-              sed 's|spring.datasource.mysql.password=.*|spring.datasource.mysql.password=somepassword|' \
+              sed 's|spring.datasource.url=.*|spring.datasource.url=jdbc:mysql://cbioportal-database:3306/cbioportal?useSSL=false|' | \
+              sed 's|spring.datasource.username=.*|spring.datasource.username=cbio_user|' | \
+              sed 's|spring.datasource.password=.*|spring.datasource.password=somepassword|' \
               > application.properties
       - name: 'Copy cgds.sql file into Docker Compose'
         run: cp ./cbioportal/src/main/resources/db-scripts/cgds.sql ./cbioportal-docker-compose/data/.

src/main/java/org/cbioportal/persistence/mybatis/UnImplementedStudyViewMyBatisRepository.java

@@ -0,0 +1,198 @@
+package org.cbioportal.persistence.mybatis;
+
+import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.CaseListDataCount;
+import org.cbioportal.model.ClinicalAttribute;
+import org.cbioportal.model.ClinicalData;
+import org.cbioportal.model.ClinicalDataCount;
+import org.cbioportal.model.ClinicalDataCountItem;
+import org.cbioportal.model.ClinicalEventTypeCount;
+import org.cbioportal.model.CopyNumberCountByGene;
+import org.cbioportal.model.GenericAssayDataCountItem;
+import org.cbioportal.model.GenomicDataCount;
+import org.cbioportal.model.GenomicDataCountItem;
+import org.cbioportal.model.MolecularProfile;
+import org.cbioportal.model.PatientTreatment;
+import org.cbioportal.model.Sample;
+import org.cbioportal.model.SampleTreatment;
+import org.cbioportal.model.StudyViewFilterContext;
+import org.cbioportal.persistence.StudyViewRepository;
+import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
+import org.cbioportal.web.parameter.ClinicalDataType;
+import org.cbioportal.web.parameter.GenericAssayDataBinFilter;
+import org.cbioportal.web.parameter.GenericAssayDataFilter;
+import org.cbioportal.web.parameter.GenomicDataBinFilter;
+import org.cbioportal.web.parameter.GenomicDataFilter;
+import org.springframework.stereotype.Repository;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+@Repository
+@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "false", matchIfMissing = true)
+public class UnImplementedStudyViewMyBatisRepository implements StudyViewRepository {
+
+    private static final String UNSUPPORTED_OPERATION = "StudyViewRepository Feature Not supported...  Contact cbio admin.";
+
+    @Override
+    public List<Sample> getFilteredSamples(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<String> getFilteredStudyIds(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<ClinicalData> getSampleClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+
+    }
+
+    @Override
+    public List<AlterationCountByGene> getMutatedGenes(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<GenomicDataCount> getMolecularProfileSampleCounts(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap() {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<CaseListDataCount> getCaseListDataCountsPerStudy(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public Map<String, Integer> getTotalProfiledCounts(StudyViewFilterContext studyViewFilterContext, String alterationType, List<MolecularProfile> molecularProfiles) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<ClinicalAttribute> getClinicalAttributes() {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<ClinicalAttribute> getClinicalAttributesForStudies(List<String> studyIds) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public int getFilteredSamplesCount(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public int getFilteredPatientCount(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilterContext studyViewFilterContext, String alterationType) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public int getTotalProfiledCountsByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public int getSampleProfileCountWithoutPanelData(StudyViewFilterContext studyViewFilterContext, String alterationType) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<PatientTreatment> getPatientTreatments(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public int getTotalPatientTreatmentCount(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<SampleTreatment> getSampleTreatments(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public int getTotalSampleTreatmentCount(StudyViewFilterContext studyViewFilterContext) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<GenomicDataCountItem> getCNACounts(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<GenericAssayDataCountItem> getGenericAssayDataCounts(StudyViewFilterContext studyViewFilterContext, List<GenericAssayDataFilter> genericAssayDataFilters) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public Map<String, Integer> getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter) {
+        throw new UnsupportedOperationException(UNSUPPORTED_OPERATION);
+    }
+
+    @Override
+    public List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters) {
+        return List.of();
+    }
+
+    @Override
+    public List<ClinicalDataCount> getGenomicDataBinCounts(StudyViewFilterContext studyViewFilterContext, List<GenomicDataBinFilter> genomicDataBinFilters) {
+        return List.of();
+    }
+
+    @Override
+    public List<ClinicalDataCount> getGenericAssayDataBinCounts(StudyViewFilterContext studyViewFilterContext, List<GenericAssayDataBinFilter> genericAssayDataBinFilters) {
+        return List.of();
+    }
+
+    @Override
+    public List<MolecularProfile> getGenericAssayProfiles() {
+        return List.of();
+    }
+
+    @Override
+    public List<MolecularProfile> getFilteredMolecularProfilesByAlterationType(StudyViewFilterContext studyViewFilterContext, String alterationType) {
+        return List.of();
+    }
+}

src/main/java/org/cbioportal/persistence/mybatis/config/PersistenceConfig.java

@@ -2,6 +2,7 @@
 
 import org.cbioportal.model.Sample;
 import org.cbioportal.persistence.mybatis.typehandler.SampleTypeTypeHandler;
+import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
 import org.mybatis.spring.SqlSessionFactoryBean;
 import org.mybatis.spring.annotation.MapperScan;
 import org.mybatis.spring.boot.autoconfigure.ConfigurationCustomizer;
@@ -33,7 +34,19 @@ public void customize(org.apache.ibatis.session.Configuration configuration) {
     }
 
     @Bean("sqlSessionFactory")
-    public SqlSessionFactoryBean sqlSessionFactory(@Qualifier("mysqlDataSource") DataSource dataSource, ApplicationContext applicationContext) throws IOException {
+    @ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true")
+    public SqlSessionFactoryBean sqlSessionFactorySpecifyDataSource(@Qualifier("mysqlDataSource") DataSource dataSource, ApplicationContext applicationContext) throws IOException {
+        return sqlSessionFactory(dataSource, applicationContext);
+    }
+
+    @Bean("sqlSessionFactory")
+    @ConditionalOnProperty(name = "clickhouse_mode", havingValue = "false", matchIfMissing = true)
+    public SqlSessionFactoryBean sqlSessionFactoryDefault(DataSource dataSource, ApplicationContext applicationContext) throws IOException {
+        return sqlSessionFactory(dataSource, applicationContext);
+    }
+
+
+    private SqlSessionFactoryBean sqlSessionFactory(DataSource dataSource, ApplicationContext applicationContext) throws IOException {
         SqlSessionFactoryBean sessionFactory = new SqlSessionFactoryBean();
         sessionFactory.setDataSource(dataSource);
         sessionFactory.setMapperLocations(
@@ -43,8 +56,9 @@ public SqlSessionFactoryBean sqlSessionFactory(@Qualifier("mysqlDataSource") Dat
         return sessionFactory;
     }
 
-        @Bean
-        public DataSourceTransactionManager transactionManager(@Qualifier("mysqlDataSource") DataSource dataSource) {
-            return new DataSourceTransactionManager(dataSource);
-        }
+    @Bean
+    @ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true")
+    public DataSourceTransactionManager transactionManager(@Qualifier("mysqlDataSource") DataSource dataSource) {
+        return new DataSourceTransactionManager(dataSource);
+    }
 }

src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java

@@ -21,6 +21,7 @@
 import org.cbioportal.persistence.helper.AlterationFilterHelper;
 import org.cbioportal.persistence.helper.StudyViewFilterHelper;
 import org.cbioportal.service.util.StudyViewColumnarServiceUtil;
+import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.GenericAssayDataBinFilter;
 import org.cbioportal.web.parameter.GenericAssayDataFilter;
@@ -38,6 +39,7 @@
 import java.util.stream.Collectors;
 
 @Repository
+@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true")
 public class StudyViewMyBatisRepository implements StudyViewRepository {
 
     private final StudyViewMapper studyViewMapper;

src/main/java/org/cbioportal/persistence/mybatisclickhouse/config/PersistenceColumnarConfig.java

@@ -1,6 +1,7 @@
 package org.cbioportal.persistence.mybatisclickhouse.config;
 
 import org.cbioportal.persistence.mybatis.typehandler.SampleTypeTypeHandler;
+import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
 import org.mybatis.spring.SqlSessionFactoryBean;
 import org.mybatis.spring.annotation.MapperScan;
 import org.springframework.beans.factory.annotation.Qualifier;
@@ -13,6 +14,7 @@
 
 
 @Configuration
+@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true")
 @MapperScan(value= "org.cbioportal.persistence.mybatisclickhouse", sqlSessionFactoryRef ="sqlColumnarSessionFactory")
 public class PersistenceColumnarConfig {
 

src/main/java/org/cbioportal/properties/CustomDataSourceConfiguration.java

@@ -1,6 +1,6 @@
 package org.cbioportal.properties;
 
-import org.springframework.beans.factory.annotation.Qualifier;
+import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
 import org.springframework.boot.autoconfigure.jdbc.DataSourceProperties;
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.context.annotation.Bean;
@@ -9,6 +9,7 @@
 import javax.sql.DataSource;
 
 @Configuration
+@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true")
 public class CustomDataSourceConfiguration {
     @Bean
     @ConfigurationProperties("spring.datasource.mysql")

src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java

@@ -21,6 +21,7 @@
 import org.cbioportal.service.exception.StudyNotFoundException;
 import org.cbioportal.service.treatment.TreatmentCountReportService;
 import org.cbioportal.service.util.StudyViewColumnarServiceUtil;
+import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.CustomSampleIdentifier;
 import org.cbioportal.web.parameter.GenericAssayDataBinFilter;
@@ -38,6 +39,7 @@
 import java.util.stream.Collectors;
 
 @Service
+@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true")
 public class StudyViewColumnarServiceImpl implements StudyViewColumnarService {
 
 

src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java

@@ -6,13 +6,15 @@
 import org.cbioportal.model.StudyViewFilterContext;
 import org.cbioportal.model.TemporalRelation;
 import org.cbioportal.persistence.StudyViewRepository;
+import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
 import java.util.Set;
 import java.util.stream.Stream;
 
 @Service
+@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true")
 public class TreatmentCountReportServiceImpl implements TreatmentCountReportService {
 
     private final StudyViewRepository studyViewRepository;

src/main/java/org/cbioportal/web/columnar/BasicDataBinner.java

@@ -4,6 +4,7 @@
 import org.cbioportal.service.CustomDataService;
 import org.cbioportal.service.StudyViewColumnarService;
 import org.cbioportal.service.util.CustomDataSession;
+import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
 import org.cbioportal.web.columnar.util.CustomDataFilterUtil;
 import org.cbioportal.web.columnar.util.NewClinicalDataBinUtil;
 import org.cbioportal.web.parameter.*;
@@ -25,6 +26,7 @@
 // but BasicDataBinner can support clinical data counts too
 // after we switched clinical data counts to use this, then We can remove ClinicalDataBinner
 @Component
+@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true")
 public class BasicDataBinner {
     private final StudyViewColumnarService studyViewColumnarService;
     private final DataBinner dataBinner;

src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java

@@ -6,6 +6,7 @@
 import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.ClinicalDataCountItem;
 import org.cbioportal.service.StudyViewColumnarService;
+import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
 import org.cbioportal.web.columnar.util.NewClinicalDataBinUtil;
 import org.cbioportal.web.parameter.ClinicalDataBinCountFilter;
 import org.cbioportal.web.parameter.ClinicalDataBinFilter;
@@ -21,6 +22,7 @@
 import java.util.stream.Collectors;
 
 @Component
+@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true")
 public class ClinicalDataBinner {
     private final StudyViewColumnarService studyViewColumnarService;
     private final DataBinner dataBinner;

src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java

@@ -33,6 +33,7 @@
 import org.cbioportal.service.ViolinPlotService;
 import org.cbioportal.service.exception.StudyNotFoundException;
 import org.cbioportal.service.util.CustomDataSession;
+import org.cbioportal.utils.config.annotation.ConditionalOnProperty;
 import org.cbioportal.web.columnar.util.CustomDataFilterUtil;
 import org.cbioportal.web.columnar.util.NewStudyViewFilterUtil;
 import org.cbioportal.web.config.annotation.InternalApi;
@@ -78,6 +79,7 @@
 @RestController()
 @RequestMapping("/api")
 @Validated
+@ConditionalOnProperty(name = "clickhouse_mode", havingValue = "true")
 public class StudyViewColumnStoreController {
 
     private final StudyViewColumnarService studyViewColumnarService;