Add resource-data-all endpoint and MyBatis SQL methods

cBioPortal · Oct 7, 2024 · 728951c · 728951c
1 parent 74516be
commit 728951c
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Showing 7 changed files with 120 additions and 1 deletion.
diff --git a/src/main/java/org/cbioportal/persistence/ResourceDataRepository.java b/src/main/java/org/cbioportal/persistence/ResourceDataRepository.java
@@ -18,5 +18,12 @@ 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);
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMapper.java b/src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMapper.java
@@ -15,4 +15,10 @@ 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);
+
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatis/ResourceDataMyBatisRepository.java
@@ -38,4 +38,20 @@ 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);
+    }
+
 }
diff --git a/src/main/java/org/cbioportal/service/ResourceDataService.java b/src/main/java/org/cbioportal/service/ResourceDataService.java
@@ -20,4 +20,7 @@ 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;
+
 }
diff --git a/src/main/java/org/cbioportal/service/impl/ResourceDataServiceImpl.java b/src/main/java/org/cbioportal/service/impl/ResourceDataServiceImpl.java
@@ -1,6 +1,7 @@
 package org.cbioportal.service.impl;
 
 import java.util.List;
+import java.util.ArrayList;
 
 import org.cbioportal.model.ResourceData;
 import org.cbioportal.persistence.ResourceDataRepository;
@@ -56,5 +57,22 @@ 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;
+    }
 
 }
diff --git a/src/main/java/org/cbioportal/web/ResourceDataController.java b/src/main/java/org/cbioportal/web/ResourceDataController.java
@@ -157,4 +157,39 @@ public ResponseEntity<List<ResourceData>> getAllStudyResourceDataInStudy(
         }
     }
 
+    // NEW COMBINED GET METHOD FOR RESOURCE-DATA
+    @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<>(
+                    resourceDataService.getAllResourceDataForStudyPatientSample(studyId, resourceId, projection.name(), pageSize, pageNumber,
+                    sortBy == null ? null : sortBy.getOriginalValue(), direction.name()), HttpStatus.OK);
+        }
+    }
+
 }
diff --git a/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDataMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatis/ResourceDataMapper.xml
@@ -171,4 +171,38 @@
         </if>
     </select>
 
-</mapper>
+    <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  
+        <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  
+        <include refid="whereStudy"/>
+    </select>
+
+</mapper>