Add Columnar Study View Controller /api/column-store

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

@@ -6,6 +6,7 @@
 import org.mybatis.spring.annotation.MapperScan;
 import org.mybatis.spring.boot.autoconfigure.ConfigurationCustomizer;
 import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
@@ -15,7 +16,7 @@
 
 
 @Configuration
-@MapperScan("org.cbioportal.persistence.mybatis")
+@MapperScan(value="org.cbioportal.persistence.mybatis", sqlSessionFactoryRef="sqlSessionFactory")
 public class PersistenceConfig {
 
     // This is the only way I was able to register the SampleType TypeHandler to MyBatis.
@@ -31,7 +32,7 @@ public void customize(org.apache.ibatis.session.Configuration configuration) {
         };
     }
 
-    @Bean
+    @Bean("sqlSessionFactory")
     public SqlSessionFactoryBean sqlSessionFactory(@Qualifier("mysqlDataSource") DataSource dataSource, ApplicationContext applicationContext) throws IOException {
         SqlSessionFactoryBean sessionFactory = new SqlSessionFactoryBean();
         sessionFactory.setDataSource(dataSource);

src/main/java/org/cbioportal/persistence/mybatiscolumnar/config/PersistenceConfig.java → src/main/java/org/cbioportal/persistence/mybatiscolumnar/config/PersistenceColumnarConfig.java

@@ -13,11 +13,11 @@
 
 
 @Configuration
-@MapperScan("org.cbioportal.persistence.mybatiscolumnar")
-public class PersistenceConfig {
+@MapperScan(value="org.cbioportal.persistence.mybatiscolumnar", sqlSessionFactoryRef ="sqlColumnarSessionFactory")
+public class PersistenceColumnarConfig {
 
-    @Bean
-    public SqlSessionFactoryBean sqlSessionFactory(@Qualifier("columnarDataSource") DataSource dataSource, ApplicationContext applicationContext) throws IOException {
+    @Bean("sqlColumnarSessionFactory")
+    public SqlSessionFactoryBean sqlColumnarSessionFactory(@Qualifier("columnarDataSource") DataSource dataSource, ApplicationContext applicationContext) throws IOException {
         SqlSessionFactoryBean sessionFactory = new SqlSessionFactoryBean();
         sessionFactory.setDataSource(dataSource);
         sessionFactory.setMapperLocations(

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

@@ -0,0 +1,22 @@
+package org.cbioportal.service;
+
+import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.ClinicalData;
+import org.cbioportal.model.ClinicalDataCountItem;
+import org.cbioportal.model.Sample;
+import org.cbioportal.web.parameter.StudyViewFilter;
+
+import java.util.List;
+
+public interface StudyViewColumnarService {
+
+    List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter);
+
+    List<AlterationCountByGene> getMutatedGenes(StudyViewFilter interceptedStudyViewFilter);
+
+    List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes);
+
+    List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds);
+
+    List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds);
+}

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

@@ -0,0 +1,114 @@
+package org.cbioportal.service.impl;
+
+import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.ClinicalData;
+import org.cbioportal.model.ClinicalDataCount;
+import org.cbioportal.model.ClinicalDataCountItem;
+import org.cbioportal.model.Sample;
+import org.cbioportal.persistence.StudyViewRepository;
+import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
+import org.cbioportal.persistence.enums.ClinicalAttributeDataType;
+import org.cbioportal.service.StudyViewColumnarService;
+import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
+import org.cbioportal.web.parameter.StudyViewFilter;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+@Service
+public class StudyViewColumnarServiceImpl implements StudyViewColumnarService {
+
+    private final Map<String, List<String>> clinicalAttributeNameMap = new HashMap<>();
+
+
+    private final StudyViewRepository studyViewRepository;
+
+    @Autowired
+    public StudyViewColumnarServiceImpl(StudyViewRepository studyViewRepository) {
+        this.studyViewRepository = studyViewRepository;
+    }
+
+    @Override
+    public List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
+        return studyViewRepository.getFilteredSamples(studyViewFilter, categorizedClinicalDataCountFilter);    
+    }
+
+    @Override
+    public List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
+        return studyViewRepository.getMutatedGenes(studyViewFilter, categorizedClinicalDataCountFilter);
+    }
+
+    @Override
+    public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
+
+        return studyViewRepository.getClinicalDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, filteredAttributes)
+            .stream().collect(Collectors.groupingBy(ClinicalDataCount::getAttributeId))
+            .entrySet().parallelStream().map(e -> {
+                ClinicalDataCountItem item = new ClinicalDataCountItem();
+                item.setAttributeId(e.getKey());
+                item.setCounts(e.getValue());
+                return item;
+            }).collect(Collectors.toList());
+    }
+
+    private CategorizedClinicalDataCountFilter extractClinicalDataCountFilters(final StudyViewFilter studyViewFilter) {
+        if(clinicalAttributeNameMap.isEmpty()) {
+            buildClinicalAttributeNameMap();
+        }
+
+        if(studyViewFilter.getClinicalDataFilters() == null) {
+            return CategorizedClinicalDataCountFilter.getBuilder().build();
+        }
+
+        final String patientCategoricalKey = ClinicalAttributeDataSource.PATIENT.getValue() + ClinicalAttributeDataType.CATEGORICAL.getValue();
+        final String patientNumericKey = ClinicalAttributeDataSource.PATIENT.getValue() + ClinicalAttributeDataType.NUMERIC.getValue();
+        final String sampleCategoricalKey = ClinicalAttributeDataSource.SAMPLE.getValue() + ClinicalAttributeDataType.CATEGORICAL.getValue();
+        final String sampleNumericKey = ClinicalAttributeDataSource.SAMPLE.getValue() + ClinicalAttributeDataType.NUMERIC.getValue();
+
+        return CategorizedClinicalDataCountFilter.getBuilder()
+            .setPatientCategoricalClinicalDataFilters(studyViewFilter.getClinicalDataFilters()
+                .stream().filter(clinicalDataFilter -> clinicalAttributeNameMap.get(patientCategoricalKey).contains(clinicalDataFilter.getAttributeId()))
+                .collect(Collectors.toList()))
+            .setPatientNumericalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream()
+                .filter(clinicalDataFilter -> clinicalAttributeNameMap.get(patientNumericKey).contains(clinicalDataFilter.getAttributeId()))
+                .collect(Collectors.toList()))
+            .setSampleCategoricalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream()
+                .filter(clinicalDataFilter -> clinicalAttributeNameMap.get(sampleCategoricalKey).contains(clinicalDataFilter.getAttributeId()))
+                .collect(Collectors.toList()))
+            .setSampleNumericalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream()
+                .filter(clinicalDataFilter -> clinicalAttributeNameMap.get(sampleNumericKey).contains(clinicalDataFilter.getAttributeId()))
+                .collect(Collectors.toList()))
+            .build();
+    }
+
+    private void buildClinicalAttributeNameMap() {
+        List<ClinicalAttributeDataSource> clinicalAttributeDataSources = List.of(ClinicalAttributeDataSource.values());
+        for(ClinicalAttributeDataSource clinicalAttributeDataSource : clinicalAttributeDataSources) {
+            String categoricalKey = clinicalAttributeDataSource.getValue() + ClinicalAttributeDataType.CATEGORICAL;
+            String numericKey = clinicalAttributeDataSource.getValue() + ClinicalAttributeDataType.NUMERIC;
+            clinicalAttributeNameMap.put(categoricalKey, studyViewRepository.getClinicalDataAttributeNames(clinicalAttributeDataSource, ClinicalAttributeDataType.CATEGORICAL));
+            clinicalAttributeNameMap.put(numericKey, studyViewRepository.getClinicalDataAttributeNames(clinicalAttributeDataSource, ClinicalAttributeDataType.NUMERIC));
+        }
+    }
+
+    @Override
+    public List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
+        return studyViewRepository.getPatientClinicalData(studyViewFilter, attributeIds, categorizedClinicalDataCountFilter);
+    }
+
+    @Override
+    public List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
+        return studyViewRepository.getSampleClinicalData(studyViewFilter, attributeIds, categorizedClinicalDataCountFilter);
+    }
+
+
+}

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

@@ -0,0 +1,129 @@
+package org.cbioportal.web.columnar;
+
+import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.AlterationFilter;
+import org.cbioportal.model.ClinicalDataBin;
+import org.cbioportal.model.ClinicalDataCountItem;
+import org.cbioportal.model.Sample;
+import org.cbioportal.service.StudyViewColumnarService;
+import org.cbioportal.service.StudyViewService;
+import org.cbioportal.service.exception.StudyNotFoundException;
+import org.cbioportal.web.columnar.util.NewStudyViewFilterUtil;
+import org.cbioportal.web.config.annotation.InternalApi;
+import org.cbioportal.web.parameter.ClinicalDataBinCountFilter;
+import org.cbioportal.web.parameter.ClinicalDataCountFilter;
+import org.cbioportal.web.parameter.ClinicalDataFilter;
+import org.cbioportal.web.parameter.DataBinMethod;
+import org.cbioportal.web.parameter.StudyViewFilter;
+import org.cbioportal.web.util.ClinicalDataBinUtil;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.validation.annotation.Validated;
+import org.springframework.web.bind.annotation.PostMapping;
+import org.springframework.web.bind.annotation.RequestAttribute;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.stream.Collectors;
+
+@InternalApi
+@RestController()
+@RequestMapping("/api")
+@Validated
+public class StudyViewColumnStoreController {
+
+    private final StudyViewColumnarService studyViewColumnarService;
+    private final StudyViewService studyViewService;
+    private final ClinicalDataBinUtil clinicalDataBinUtil;
+
+    @Autowired
+    public StudyViewColumnStoreController(StudyViewColumnarService studyViewColumnarService, StudyViewService studyViewService, ClinicalDataBinUtil clinicalDataBinUtil) {
+        this.studyViewColumnarService = studyViewColumnarService;
+        this.studyViewService = studyViewService;
+        this.clinicalDataBinUtil = clinicalDataBinUtil;
+    }
+
+    @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
+    @PostMapping(value = "/column-store/filtered-samples/fetch",
+        consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
+    public ResponseEntity<List<Sample>> fetchFilteredSamples(
+        @RequestParam(defaultValue = "false") Boolean negateFilters,
+        @RequestAttribute(required = false, value = "involvedCancerStudies") Collection<String> involvedCancerStudies,
+        @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter,
+        @RequestBody(required = false) StudyViewFilter studyViewFilter) {
+        return new ResponseEntity<>(
+            studyViewColumnarService.getFilteredSamples(interceptedStudyViewFilter),
+            HttpStatus.OK
+        );
+    }
+
+    @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
+    @PostMapping(value = "/column-store/mutated-genes/fetch",
+        consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
+    public ResponseEntity<List<AlterationCountByGene>> fetchMutatedGenes(
+        @RequestBody(required = false) StudyViewFilter studyViewFilter,
+        @RequestAttribute(required = false, value = "involvedCancerStudies") Collection<String> involvedCancerStudies,
+        @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter
+    ) throws StudyNotFoundException {
+        AlterationFilter annotationFilters = interceptedStudyViewFilter.getAlterationFilter();
+        List<Sample> samples = studyViewColumnarService.getFilteredSamples(interceptedStudyViewFilter);
+        List<String> studyIds = new ArrayList<>();
+        List<String> sampleIds = new ArrayList<>();
+        for(Sample sample : samples) {
+            studyIds.add(sample.getCancerStudyIdentifier());
+            sampleIds.add(sample.getStableId());
+        }
+        return new ResponseEntity<>(
+            studyViewService.getMutationAlterationCountByGenes(studyIds, sampleIds, annotationFilters),
+            HttpStatus.OK
+        );
+    }
+
+    @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
+    @PostMapping(value = "/column-store/clinical-data-counts/fetch", 
+        consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
+    public ResponseEntity<List<ClinicalDataCountItem>> fetchClinicalDataCounts(
+        @RequestBody(required = false) ClinicalDataCountFilter clinicalDataCountFilter,
+        @RequestAttribute(required = false, value = "involvedCancerStudies") Collection<String> involvedCancerStudies,
+        @RequestAttribute(required = false, value = "interceptedClinicalDataCountFilter") ClinicalDataCountFilter interceptedClinicalDataCountFilter) {
+
+        List<ClinicalDataFilter> attributes = interceptedClinicalDataCountFilter.getAttributes();
+        StudyViewFilter studyViewFilter = interceptedClinicalDataCountFilter.getStudyViewFilter();
+
+        if (attributes.size() == 1) {
+            NewStudyViewFilterUtil.removeSelfFromFilter(attributes.get(0).getAttributeId(), studyViewFilter);
+       }
+       // boolean singleStudyUnfiltered = studyViewFilterUtil.isSingleStudyUnfiltered(studyViewFilter);
+        List<ClinicalDataCountItem> result = studyViewColumnarService.getClinicalDataCounts(studyViewFilter, 
+            attributes.stream().map(ClinicalDataFilter::getAttributeId).collect(Collectors.toList()));
+            //studyIds, sampleIds, attributes.stream().map(a -> a.getAttributeId()).collect(Collectors.toList())); 
+        return new ResponseEntity<>(result, HttpStatus.OK);
+
+    }
+
+    @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
+    @RequestMapping(value = "/column-store/clinical-data-bin-counts/fetch", method = RequestMethod.POST,
+        consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
+    public ResponseEntity<List<ClinicalDataBin>> fetchClinicalDataBinCounts(
+        @RequestParam(defaultValue = "DYNAMIC") DataBinMethod dataBinMethod,
+        @RequestBody(required = false) ClinicalDataBinCountFilter clinicalDataBinCountFilter,
+        @RequestAttribute(required = false, value = "involvedCancerStudies") Collection<String> involvedCancerStudies,
+        @RequestAttribute(required = false, value = "interceptedClinicalDataBinCountFilter") ClinicalDataBinCountFilter interceptedClinicalDataBinCountFilter
+    ) {
+        List<ClinicalDataBin> clinicalDataBins = clinicalDataBinUtil.fetchClinicalDataBinCounts(
+            dataBinMethod,
+            interceptedClinicalDataBinCountFilter,
+            true
+        );
+        return new ResponseEntity<>(clinicalDataBins, HttpStatus.OK);
+    }
+}

src/main/java/org/cbioportal/web/columnar/util/NewStudyViewFilterUtil.java

@@ -0,0 +1,13 @@
+package org.cbioportal.web.columnar.util;
+
+
+import org.cbioportal.web.parameter.StudyViewFilter;
+
+public class NewStudyViewFilterUtil {
+
+    public static void removeSelfFromFilter(String attributeId, StudyViewFilter studyViewFilter) {
+        if (studyViewFilter!= null && studyViewFilter.getClinicalDataFilters() != null) {
+            studyViewFilter.getClinicalDataFilters().removeIf(f -> f.getAttributeId().equals(attributeId));
+        }
+    }
+}

src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java

@@ -35,6 +35,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import jakarta.servlet.http.HttpServletRequest;
 import jakarta.servlet.http.HttpServletResponse;
+import org.apache.commons.lang3.StringUtils;
 import org.cbioportal.model.AlterationFilter;
 import org.cbioportal.model.MolecularProfile;
 import org.cbioportal.model.MolecularProfileCaseIdentifier;
@@ -140,6 +141,7 @@ public class InvolvedCancerStudyExtractorInterceptor implements HandlerIntercept
         // reset this to  'String requestPathInfo = request.getPathInfo();'
         String requestPathInfo = request.getPathInfo() == null? request.getServletPath() : request.getPathInfo();
         requestPathInfo = requestPathInfo.replaceFirst("^/api", "");
+        requestPathInfo = StringUtils.removeStart(requestPathInfo, "/column-store");
         if (requestPathInfo.equals(PATIENT_FETCH_PATH)) {
             return extractAttributesFromPatientFilter(request);
         } else if (requestPathInfo.equals(SAMPLE_FETCH_PATH)) {

src/main/resources/org/cbioportal/persistence/mybatiscolumnar/StudyViewMapper.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE mapper PUBLIC "-//mybatis.org//DTD Mapper 3.0//EN" "http://mybatis.org/dtd/mybatis-3-mapper.dtd">
 
-<mapper namespace="org.cbioportal.persistence.mybatiscolumnstore.StudyViewMapper">
+<mapper namespace="org.cbioportal.persistence.mybatiscolumnar.StudyViewMapper">
 
     <!-- for /filtered-sample/fetch (returns Sample objects) -->
     <select id="getFilteredSamples" resultType="org.cbioportal.model.Sample">