Extract column store endpoints into StudyViewColumnStoreController (c…

…BioPortal#10245) * Extract column store endpoints into StudyViewControllerColumnStore * rename
pughlab · Nov 8, 2023 · d6756a5 · d6756a5
1 parent cfb6c7d
commit d6756a5
Show file tree

Hide file tree

Showing 3 changed files with 75 additions and 39 deletions.
diff --git a/web/src/main/java/org/cbioportal/web/StudyViewController.java b/web/src/main/java/org/cbioportal/web/StudyViewController.java
@@ -209,24 +209,6 @@ public ResponseEntity<List<AlterationCountByGene>> fetchMutatedGenes(
         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),
-            HttpStatus.OK
-        );
-    }
-
     @Cacheable(
         cacheResolver = "staticRepositoryCacheOneResolver",
         condition = "@cacheEnabledConfig.getEnabled() && #singleStudyUnfiltered"
@@ -349,26 +331,6 @@ public ResponseEntity<List<Sample>> fetchFilteredSamples(
         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
-        );
-    }
-
     @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
     @RequestMapping(value = "/molecular-profile-sample-counts/fetch", method = RequestMethod.POST,
         consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)

diff --git a/web/src/main/java/org/cbioportal/web/columnstore/StudyViewColumnStoreController.java b/web/src/main/java/org/cbioportal/web/columnstore/StudyViewColumnStoreController.java
@@ -0,0 +1,73 @@
+package org.cbioportal.web.columnstore;
+
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import io.swagger.annotations.ApiParam;
+import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.Sample;
+import org.cbioportal.service.StudyViewService;
+import org.cbioportal.web.config.annotation.InternalApi;
+import org.cbioportal.webparam.StudyViewFilter;
+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.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+import springfox.documentation.annotations.ApiIgnore;
+
+import javax.validation.Valid;
+import java.util.Collection;
+import java.util.List;
+
+@InternalApi
+@RestController
+@Validated
+@Api(tags = "Study View Column Store")
+public class StudyViewColumnStoreController {
+
+    @Autowired
+    private StudyViewService studyViewService;
+
+    @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)
+    @ApiOperation("Fetch sample IDs by study view filter")
+    public ResponseEntity<List<Sample>> fetchFilteredSamples(
+        @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
+        );
+    }
+
+    @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)
+    @ApiOperation("Fetch mutated genes by study view filter")
+    public ResponseEntity<List<AlterationCountByGene>> fetchMutatedGenes(
+        @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),
+            HttpStatus.OK
+        );
+    }
+}
diff --git a/web/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java b/web/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java
@@ -39,6 +39,7 @@
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import org.apache.commons.lang3.StringUtils;
 import org.cbioportal.model.AlterationFilter;
 import org.cbioportal.model.MolecularProfile;
 import org.cbioportal.model.MolecularProfileCaseIdentifier;
@@ -132,7 +133,7 @@ public class InvolvedCancerStudyExtractorInterceptor extends HandlerInterceptorA
         if (!request.getMethod().equals("POST")) {
             return true; // no attribute extraction needed because all user supplied filter objects are in POST requests
         }
-        String requestPathInfo = request.getPathInfo();
+        String requestPathInfo = StringUtils.removeStart(request.getPathInfo(), "/column-store");
         if (requestPathInfo.equals(PATIENT_FETCH_PATH)) {
             return extractAttributesFromPatientFilter(request);
         } else if (requestPathInfo.equals(SAMPLE_FETCH_PATH)) {