Publish virtual study by modifying it instead of making copy

Also get rid of undocumented endpoint

docs/Create-And-Publish-Virtual-Study.md

@@ -32,8 +32,6 @@ curl \
   -H 'X-PUBLISHER-API-KEY: <session.endpoint.publisher-api-key>' \
   -v 'http://<cbioportal_host>/api/public_virtual_studies/<virtual_study_id>'
 ```
-This call publishes a *copy* of the virtual study under a different ID.
-The new ID hash will be printed by the command.
 The published virtual study will appear under the `Public Virtual Studies` section (next to the `My Virtual Studies` section) on the landing page for all users of cBioPortal.
 
 While publishing, you can specify the PubMed ID (`pmid`) and `typeOfCancerId` of the virtual study using the following command:
@@ -58,7 +56,5 @@ Here is the command to un-publish a virtual study:
 curl \
   -X DELETE \
   -H 'X-PUBLISHER-API-KEY: <session.endpoint.publisher-api-key>' \
-  -v 'http://<cbioportal_host>/api/public_virtual_studies/<published_virtual_study_id>'
-```
-
-*Note*: You have to use the ID of the *published* virtual study, not the one it was copied from during the publishing process.
+  -v 'http://<cbioportal_host>/api/public_virtual_studies/<virtual_study_id>'
+```

src/main/java/org/cbioportal/service/util/SessionServiceRequestHandler.java

@@ -138,8 +138,16 @@ public void softRemoveVirtualStudy(String id) {
         VirtualStudy virtualStudy = getVirtualStudyById(id);
         VirtualStudyData data = virtualStudy.getData();
         data.setUsers(Collections.emptySet());
+        updateVirtualStudy(virtualStudy);
+    }
+
+    /**
+     * Updates virtual study
+     * @param virtualStudy - virtual study to update
+     */
+    public void updateVirtualStudy(VirtualStudy virtualStudy) {
         new RestTemplate()
-            .put(sessionServiceURL + "/virtual_study/" + id,
-                new HttpEntity<>(data, getHttpHeaders()));
+            .put(sessionServiceURL + "/virtual_study/" + virtualStudy.getId(),
+                new HttpEntity<>(virtualStudy.getData(), getHttpHeaders()));
     }
 }

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

@@ -19,7 +19,6 @@
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.PostMapping;
-import org.springframework.web.bind.annotation.RequestBody;
 import org.springframework.web.bind.annotation.RequestHeader;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestParam;
@@ -58,33 +57,17 @@ public ResponseEntity<List<VirtualStudy>> getPublicVirtualStudies() {
         return new ResponseEntity<>(virtualStudies, HttpStatus.OK);
     }
 
-    @PostMapping
-    @ApiResponse(responseCode = "200", description = "OK", content = @Content(schema = @Schema(implementation = VirtualStudy.class)))
-    public ResponseEntity<VirtualStudy> publishVirtualStudyData(
-        @RequestBody VirtualStudyData virtualStudyData,
-        @RequestHeader(value = "X-PUBLISHER-API-KEY") String providedPublisherApiKey,
-        @RequestParam(required = false) String typeOfCancerId,
-        @RequestParam(required = false) String pmid
-    ) {
-        ensureProvidedPublisherApiKeyCorrect(providedPublisherApiKey);
-        VirtualStudyData virtualStudyDataToPublish = makeCopyForPublishing(virtualStudyData);
-        updateStudyMetadataFieldsIfSpecified(virtualStudyDataToPublish, typeOfCancerId, pmid);
-        VirtualStudy virtualStudy = sessionServiceRequestHandler.createVirtualStudy(virtualStudyDataToPublish);
-
-        return new ResponseEntity<>(virtualStudy, HttpStatus.OK);
-    }
-
     @PostMapping("/{id}")
     @ApiResponse(responseCode = "200", description = "OK", content = @Content(schema = @Schema(implementation = VirtualStudy.class)))
-    public ResponseEntity<VirtualStudy> publishVirtualStudy(
+    public ResponseEntity<Void> publishVirtualStudy(
         @PathVariable String id,
         @RequestHeader(value = "X-PUBLISHER-API-KEY") String providedPublisherApiKey,
         @RequestParam(required = false) String typeOfCancerId,
         @RequestParam(required = false) String pmid
     ) {
         ensureProvidedPublisherApiKeyCorrect(providedPublisherApiKey);
-        VirtualStudy virtualStudy = sessionServiceRequestHandler.getVirtualStudyById(id);
-        return publishVirtualStudyData(virtualStudy.getData(), providedPublisherApiKey, typeOfCancerId, pmid);
+        publishVirtualStudy(id, typeOfCancerId, pmid);
+        return ResponseEntity.ok().build();
     }
 
     @DeleteMapping("/{id}")
@@ -98,6 +81,14 @@ public ResponseEntity<Void> retractVirtualStudy(
         return ResponseEntity.ok().build();
     }
 
+    private void publishVirtualStudy(String id, String typeOfCancerId, String pmid) {
+        VirtualStudy virtualStudyDataToPublish = sessionServiceRequestHandler.getVirtualStudyById(id);
+        VirtualStudyData virtualStudyData = virtualStudyDataToPublish.getData();
+        updateStudyMetadataFieldsIfSpecified(virtualStudyData, typeOfCancerId, pmid);
+        virtualStudyData.setUsers(Set.of(ALL_USERS));
+        sessionServiceRequestHandler.updateVirtualStudy(virtualStudyDataToPublish);
+    }
+
     private void ensureProvidedPublisherApiKeyCorrect(String providedPublisherApiKey) {
         if (requiredPublisherApiKey.isBlank()
             || !requiredPublisherApiKey.equals(providedPublisherApiKey)) {
@@ -120,15 +111,4 @@ private void updateStudyMetadataFieldsIfSpecified(VirtualStudyData virtualStudyD
         }
     }
 
-    private VirtualStudyData makeCopyForPublishing(VirtualStudyData virtualStudyData) {
-        VirtualStudyData virtualStudyDataToPublish = new VirtualStudyData();
-        virtualStudyDataToPublish.setName(virtualStudyData.getName());
-        virtualStudyDataToPublish.setDescription(virtualStudyData.getDescription());
-        virtualStudyDataToPublish.setStudies(virtualStudyData.getStudies());
-        virtualStudyDataToPublish.setStudyViewFilter(virtualStudyData.getStudyViewFilter());
-        virtualStudyDataToPublish.setTypeOfCancerId(virtualStudyData.getTypeOfCancerId());
-        virtualStudyDataToPublish.setPmid(virtualStudyData.getPmid());
-        virtualStudyDataToPublish.setUsers(Set.of(ALL_USERS));
-        return virtualStudyDataToPublish;
-    }
 }

src/test/java/org/cbioportal/test/integration/PublicVirtualStudiesIntegrationTest.java

@@ -76,8 +76,7 @@ public class PublicVirtualStudiesIntegrationTest extends ContainerConfig {
     static final ParameterizedTypeReference<List<VirtualStudy>> typeRef = new ParameterizedTypeReference<>() {
     };
 
-    static String createdVsId;
-    static String publishedVsId;
+    static String virtualStudyId;
 
     static final VirtualStudyData virtualStudyDataToSave = createTestVsData();
 
@@ -107,35 +106,32 @@ public void test2CreateVirtualStudy() {
         assertThat(response2.getStatusCode().is2xxSuccessful()).isTrue();
         VirtualStudy savedVs = response2.getBody();
         assertThat(savedVs).isNotNull().hasFieldOrProperty("id").isNotNull();
-        createdVsId = savedVs.getId();
+        virtualStudyId = savedVs.getId();
     }
 
     @Test
     public void test3PublishVirtualStudy() {
-        String url = CBIO_URL + "/api/public_virtual_studies/" + createdVsId + "?typeOfCancerId=acc&pmid=12345";
-        ResponseEntity<VirtualStudy> response3 = restTemplate.exchange(
+        String url = CBIO_URL + "/api/public_virtual_studies/" + virtualStudyId + "?typeOfCancerId=acc&pmid=12345";
+        ResponseEntity<Void> response3 = restTemplate.exchange(
             url,
             HttpMethod.POST,
             null,
-            VirtualStudy.class);
+            Void.class);
         assertThat(response3.getStatusCode()).isEqualTo(HttpStatus.BAD_REQUEST);
 
         response3 = restTemplate.exchange(
             url,
             HttpMethod.POST,
             new HttpEntity<>(null, invalidKeyContainingHeaders),
-            VirtualStudy.class);
+            Void.class);
         assertThat(response3.getStatusCode()).isEqualTo(HttpStatus.UNAUTHORIZED);
 
         response3 = restTemplate.exchange(
             url,
             HttpMethod.POST,
             new HttpEntity<>(null, validKeyContainingHeaders),
-            VirtualStudy.class);
+            Void.class);
         assertThat(response3.getStatusCode().is2xxSuccessful()).isTrue();
-        VirtualStudy publishedVs = response3.getBody();
-        assertThat(publishedVs).isNotNull();
-        publishedVsId = publishedVs.getId();
     }
 
     @Test
@@ -163,21 +159,21 @@ public void test4ListJustPublishedStudy() {
     @Test
     public void test5UnpublishVirtualStudy() {
         ResponseEntity<Object> response5 = restTemplate.exchange(
-            CBIO_URL + "/api/public_virtual_studies/" + publishedVsId,
+            CBIO_URL + "/api/public_virtual_studies/" + virtualStudyId,
             HttpMethod.DELETE,
             null,
             Object.class);
         assertThat(response5.getStatusCode()).isEqualTo(HttpStatus.BAD_REQUEST);
 
         response5 = restTemplate.exchange(
-            CBIO_URL + "/api/public_virtual_studies/" + publishedVsId,
+            CBIO_URL + "/api/public_virtual_studies/" + virtualStudyId,
             HttpMethod.DELETE,
             new HttpEntity<>(null, invalidKeyContainingHeaders),
             Object.class);
         assertThat(response5.getStatusCode()).isEqualTo(HttpStatus.UNAUTHORIZED);
 
         response5 = restTemplate.exchange(
-            CBIO_URL + "/api/public_virtual_studies/" + publishedVsId,
+            CBIO_URL + "/api/public_virtual_studies/" + virtualStudyId,
             HttpMethod.DELETE,
             new HttpEntity<>(null, validKeyContainingHeaders),
             Object.class);