Revert original Study View endpoints (cBioPortal#10216)

* revert study view controller original endpoints and rename clickhouse endpoints * add mybatiscolumnstore to test application context
pughlab · Nov 8, 2023 · cfb6c7d · cfb6c7d
1 parent c1bdbda
commit cfb6c7d
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Showing 2 changed files with 45 additions and 1 deletion.
diff --git a/core/src/test/resources/applicationContext-dao.xml b/core/src/test/resources/applicationContext-dao.xml
@@ -90,7 +90,7 @@
 
     <!-- scan for mappers and let them be autowired -->
     <bean class="org.mybatis.spring.mapper.MapperScannerConfigurer">
-        <property name="basePackage" value="org.mskcc.cbio.portal.persistence,org.cbioportal.persistence.mybatis" />
+        <property name="basePackage" value="org.mskcc.cbio.portal.persistence,org.cbioportal.persistence.mybatis,org.cbioportal.persistence.mybatiscolumnstore" />
     </bean>
 
     <!-- enable component scanning (beware that this does not enable mapper scanning!) -->

diff --git a/web/src/main/java/org/cbioportal/web/StudyViewController.java b/web/src/main/java/org/cbioportal/web/StudyViewController.java
@@ -203,6 +203,23 @@ public ResponseEntity<List<AlterationCountByGene>> fetchMutatedGenes(
         @RequestAttribute(required = false, value = "involvedCancerStudies") Collection<String> involvedCancerStudies,
         @ApiIgnore // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above.
         @Valid @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter
+    ) throws StudyNotFoundException {
+        boolean singleStudyUnfiltered = studyViewFilterUtil.isSingleStudyUnfiltered(interceptedStudyViewFilter);
+        List<AlterationCountByGene> alterationCountByGenes = instance.cachedFetchMutatedGenes(interceptedStudyViewFilter, singleStudyUnfiltered);
+        return new ResponseEntity<>(alterationCountByGenes, HttpStatus.OK);
+    }
+
+    @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
+    @RequestMapping(value = "/column-store/mutated-genes/fetch", method = RequestMethod.POST,
+        consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
+    @ApiOperation("Fetch mutated genes by study view filter")
+    public ResponseEntity<List<AlterationCountByGene>> fetchMutatedGenesFromColumnStore(
+        @ApiParam(required = true, value = "Study view filter")
+        @Valid @RequestBody(required = false) StudyViewFilter studyViewFilter,
+        @ApiIgnore // prevent reference to this attribute in the swagger-ui interface
+        @RequestAttribute(required = false, value = "involvedCancerStudies") Collection<String> involvedCancerStudies,
+        @ApiIgnore // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above.
+        @Valid @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter
     ) {
         return new ResponseEntity<>(
             studyViewService.getMutatedGenesFromColumnstore(interceptedStudyViewFilter),
@@ -319,6 +336,33 @@ public ResponseEntity<List<Sample>> fetchFilteredSamples(
         @ApiParam(required = true, value = "Study view filter")
         @Valid @RequestBody(required = false) StudyViewFilter studyViewFilter) {
 
+        List<String> studyIds = new ArrayList<>();
+        List<String> sampleIds = new ArrayList<>();
+
+        studyViewFilterUtil.extractStudyAndSampleIds(
+            studyViewFilterApplier.apply(interceptedStudyViewFilter, negateFilters), studyIds, sampleIds);
+
+        List<Sample> result = new ArrayList<>();
+        if (!sampleIds.isEmpty()) {
+            result = sampleService.fetchSamples(studyIds, sampleIds, Projection.ID.name());
+        }
+        return new ResponseEntity<>(result, HttpStatus.OK);
+    }
+
+    @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
+    @RequestMapping(value = "/column-store/filtered-samples/fetch", method = RequestMethod.POST,
+        consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
+    @ApiOperation("Fetch sample IDs by study view filter")
+    public ResponseEntity<List<Sample>> fetchFilteredSamplesFromColumnStore(
+        @ApiParam("Whether to negate the study view filters")
+        @RequestParam(defaultValue = "false") Boolean negateFilters,
+        @ApiIgnore // prevent reference to this attribute in the swagger-ui interface
+        @RequestAttribute(required = false, value = "involvedCancerStudies") Collection<String> involvedCancerStudies,
+        @ApiIgnore // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above.
+        @Valid @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter,
+        @ApiParam(required = true, value = "Study view filter")
+        @Valid @RequestBody(required = false) StudyViewFilter studyViewFilter) {
+
         return new ResponseEntity<>(
             studyViewService.getFilteredSamplesFromColumnstore(interceptedStudyViewFilter),
             HttpStatus.OK