Revert "Merge pull request #11051 from hweej/11004/resource-data-expa…

…nd-all-results"

This reverts commit 8e1a02b, reversing
changes made to 2284f83.

src/main/java/org/cbioportal/persistence/ResourceDataRepository.java

@@ -18,12 +18,5 @@ List<ResourceData> getAllResourceDataOfPatientInStudy(String studyId, String pat
     @Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()")
     List<ResourceData> getAllResourceDataForStudy(String studyId, String resourceId, String projection,
             Integer pageSize, Integer pageNumber, String sortBy, String direction);
-
-    @Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()")
-    List<ResourceData> getResourceDataForAllPatientsInStudy(String studyId, String resourceId, String projection,
-            Integer pageSize, Integer pageNumber, String sortBy, String direction);
 
-    @Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()")
-    List<ResourceData> getResourceDataForAllSamplesInStudy(String studyId, String resourceId, String projection,
-            Integer pageSize, Integer pageNumber, String sortBy, String direction);
 }

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

@@ -15,10 +15,4 @@ List<ResourceData> getResourceDataOfPatientInStudy(String studyId, String patien
     List<ResourceData> getResourceDataForStudy(String studyId, String resourceId, String projection, Integer limit,
             Integer offset, String sortBy, String direction);
 
-    List<ResourceData> getResourceDataForAllPatientsInStudy(String studyId, String resourceId, String projection, Integer limit,
-            Integer offset, String sortBy, String direction);
-
-    List<ResourceData> getResourceDataForAllSamplesInStudy(String studyId, String resourceId, String projection, Integer limit,
-            Integer offset, String sortBy, String direction);
-
 }

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

@@ -38,20 +38,4 @@ public List<ResourceData> getAllResourceDataForStudy(String studyId, String reso
                 PaginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
     }
 
-    @Override
-    public List<ResourceData> getResourceDataForAllPatientsInStudy(String studyId, String resourceId, String projection,
-            Integer pageSize, Integer pageNumber, String sortBy, String direction) {
-
-        return resourceDataMapper.getResourceDataForAllPatientsInStudy(studyId, resourceId, projection, pageSize,
-                PaginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
-    }
-
-    @Override
-    public List<ResourceData> getResourceDataForAllSamplesInStudy(String studyId, String resourceId, String projection,
-            Integer pageSize, Integer pageNumber, String sortBy, String direction) {
-
-        return resourceDataMapper.getResourceDataForAllSamplesInStudy(studyId, resourceId, projection, pageSize,
-                PaginationCalculator.offset(pageSize, pageNumber), sortBy, direction);
-    }
-
 }

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

@@ -20,7 +20,4 @@ List<ResourceData> getAllResourceDataOfPatientInStudy(String studyId, String pat
     List<ResourceData> getAllResourceDataForStudy(String studyId, String resourceId, String projection,
             Integer pageSize, Integer pageNumber, String sortBy, String direction) throws StudyNotFoundException;
 
-    List<ResourceData> getAllResourceDataForStudyPatientSample(String studyId, String resourceId, String projection,
-            Integer pageSize, Integer pageNumber, String sortBy, String direction) throws StudyNotFoundException;
-
 }

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

@@ -1,7 +1,6 @@
 package org.cbioportal.service.impl;
 
 import java.util.List;
-import java.util.ArrayList;
 
 import org.cbioportal.model.ResourceData;
 import org.cbioportal.persistence.ResourceDataRepository;
@@ -57,22 +56,5 @@ public List<ResourceData> getAllResourceDataForStudy(String studyId, String reso
         return resourceDataRepository.getAllResourceDataForStudy(studyId, resourceId, projection, pageSize, pageNumber,
                 sortBy, direction);
     }
-
-    @Override
-    public List<ResourceData> getAllResourceDataForStudyPatientSample(String studyId, String resourceId, String projection,
-            Integer pageSize, Integer pageNumber, String sortBy, String direction) throws StudyNotFoundException {
-
-        studyService.getStudy(studyId);
-
-        List<ResourceData> results = new ArrayList<ResourceData>();
-
-        results.addAll(resourceDataRepository.getAllResourceDataForStudy(studyId, resourceId, projection, pageSize, pageNumber,
-                sortBy, direction));
-        results.addAll(resourceDataRepository.getResourceDataForAllPatientsInStudy(studyId, resourceId, projection, pageSize, pageNumber,
-                sortBy, direction));
-        results.addAll(resourceDataRepository.getResourceDataForAllSamplesInStudy(studyId, resourceId, projection, pageSize, pageNumber,
-               sortBy, direction));
-        return results;
-    }
 
 }

src/main/java/org/cbioportal/web/ResourceDataController.java

@@ -9,7 +9,6 @@
 import io.swagger.v3.oas.annotations.tags.Tag;
 import jakarta.validation.constraints.Max;
 import jakarta.validation.constraints.Min;
-
 import org.cbioportal.model.ResourceData;
 import org.cbioportal.service.ResourceDataService;
 import org.cbioportal.service.exception.PatientNotFoundException;
@@ -22,8 +21,6 @@
 import org.cbioportal.web.parameter.Projection;
 import org.cbioportal.web.parameter.sort.ResourceDataSortBy;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.ApplicationContext;
-import org.springframework.cache.annotation.Cacheable;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
@@ -36,7 +33,6 @@
 import org.springframework.web.bind.annotation.RestController;
 
 import java.util.List;
-import java.util.Objects;
 
 @InternalApi
 @RestController()
@@ -51,17 +47,6 @@ public class ResourceDataController {
     @Autowired
     private ResourceDataService resourceDataService;
 
-    @Autowired
-    private ApplicationContext applicationContext;
-    ResourceDataController instance;
-
-    private ResourceDataController getInstance() {
-        if (Objects.isNull(instance)) {
-            instance = applicationContext.getBean(ResourceDataController.class);
-        }
-        return instance;
-    }
-
     @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)")
     @RequestMapping(value = "/studies/{studyId}/samples/{sampleId}/resource-data", method = RequestMethod.GET,
         produces = MediaType.APPLICATION_JSON_VALUE)
@@ -172,49 +157,4 @@ public ResponseEntity<List<ResourceData>> getAllStudyResourceDataInStudy(
         }
     }
 
-    @PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)")
-    @RequestMapping(value = "/studies/{studyId}/resource-data-all", method = RequestMethod.GET,
-        produces = MediaType.APPLICATION_JSON_VALUE)
-    @Operation(description = "Get all resource data for for all patients and all samples within a study")
-    @ApiResponse(responseCode = "200", description = "OK",
-        content = @Content(array = @ArraySchema(schema = @Schema(implementation = ResourceData.class))))
-    public ResponseEntity<List<ResourceData>> getAllStudyResourceDataInStudyPatientSample(
-        @Parameter(required = true, description = "Study ID e.g. acc_tcga")
-        @PathVariable String studyId,
-        @Parameter(description = "Resource ID")
-        @RequestParam(required = false) String resourceId,
-        @Parameter(description = "Level of detail of the response")
-        @RequestParam(defaultValue = "SUMMARY") Projection projection,
-        @Parameter(description = "Page size of the result list")
-        @Max(RESOURCE_DATA_MAX_PAGE_SIZE)
-        @Min(PagingConstants.MIN_PAGE_SIZE)
-        @RequestParam(defaultValue = RESOURCE_DATA_DEFAULT_PAGE_SIZE) Integer pageSize,
-        @Parameter(description = "Page number of the result list")
-        @Min(PagingConstants.MIN_PAGE_NUMBER)
-        @RequestParam(defaultValue = PagingConstants.DEFAULT_PAGE_NUMBER) Integer pageNumber,
-        @Parameter(description = "Name of the property that the result list is sorted by")
-        @RequestParam(required = false) ResourceDataSortBy sortBy,
-        @Parameter(description = "Direction of the sort")
-        @RequestParam(defaultValue = "ASC") Direction direction) throws StudyNotFoundException {
-
-        if (projection == Projection.META) {
-            throw new UnsupportedOperationException("Requested API is not implemented yet");
-        } else {
-            return new ResponseEntity<>(this.getInstance().cacheableFetchAllResourceDataForStudyPatientSample(
-                studyId, resourceId, projection.name(), pageSize, pageNumber, sortBy == null ? null : sortBy.getOriginalValue(), 
-                direction.name()) , HttpStatus.OK);
-        }
-    }
-
-    @Cacheable(
-        cacheResolver = "staticRepositoryCacheOneResolver"
-        //condition = "@cacheEnabledConfig.getEnabled() && #unfilteredQuery && (#sortBy == null || #sortBy.isEmpty())"
-    )
-    public List<ResourceData> cacheableFetchAllResourceDataForStudyPatientSample(String studyId, String resourceId, String projectionName, 
-        Integer pageSize, Integer pageNumber, String sortBy, String directionName) throws StudyNotFoundException {
-
-        return resourceDataService.getAllResourceDataForStudyPatientSample(studyId, resourceId, projectionName, pageSize, pageNumber, 
-            sortBy, directionName);
-    }
-
 }

src/main/resources/org/cbioportal/persistence/mybatis/ResourceDataMapper.xml

@@ -171,40 +171,4 @@
         </if>
     </select>
 
-    <select id="getResourceDataForAllPatientsInStudy" resultType="org.cbioportal.model.ResourceData">
-        SELECT
-        <include refid="selectPatientResource">
-            <property name="prefix" value=""/>
-        </include>
-        FROM 
-            cancer_study 
-        JOIN 
-            patient ON patient.CANCER_STUDY_ID=cancer_study.CANCER_STUDY_ID 
-        JOIN 
-            resource_patient ON resource_patient.INTERNAL_ID=patient.INTERNAL_ID 
-        JOIN 
-            resource_definition ON (resource_definition.RESOURCE_ID=resource_patient.RESOURCE_ID 
-                AND cancer_study.CANCER_STUDY_ID=resource_definition.CANCER_STUDY_ID)
-        <include refid="whereStudy"/>
-    </select>
-
-    <select id="getResourceDataForAllSamplesInStudy" resultType="org.cbioportal.model.ResourceData">
-        SELECT
-        <include refid="selectSampleResource">
-            <property name="prefix" value=""/>
-        </include>
-        FROM 
-            cancer_study 
-        JOIN 
-            patient ON patient.CANCER_STUDY_ID=cancer_study.CANCER_STUDY_ID
-        JOIN 
-            sample ON sample.PATIENT_ID=patient.INTERNAL_ID 
-        JOIN 
-            resource_sample ON resource_sample.INTERNAL_ID=sample.INTERNAL_ID 
-        JOIN 
-            resource_definition ON (resource_definition.RESOURCE_ID=resource_sample.RESOURCE_ID 
-                AND cancer_study.CANCER_STUDY_ID=resource_definition.CANCER_STUDY_ID)
-        <include refid="whereStudy"/>
-    </select>
-
-</mapper>
+</mapper>