Rfc85 dynamic virtual study

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

@@ -23,16 +23,18 @@
 import org.cbioportal.web.parameter.PageSettingsIdentifier;
 import org.cbioportal.web.parameter.PagingConstants;
 import org.cbioportal.web.parameter.ResultsPageSettings;
+import org.cbioportal.web.parameter.SampleIdentifier;
 import org.cbioportal.web.parameter.SessionPage;
 import org.cbioportal.web.parameter.StudyPageSettings;
 import org.cbioportal.web.parameter.VirtualStudy;
 import org.cbioportal.web.parameter.VirtualStudyData;
+import org.cbioportal.web.parameter.VirtualStudySamples;
+import org.cbioportal.web.util.StudyViewFilterApplier;
 import org.json.simple.JSONObject;
 import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.core.ParameterizedTypeReference;
 import org.springframework.http.HttpEntity;
@@ -57,6 +59,7 @@
 import java.util.Optional;
 import java.util.Set;
 import java.util.regex.Pattern;
+import java.util.stream.Collectors;
 
 import static org.cbioportal.web.PublicVirtualStudiesController.ALL_USERS;
 
@@ -70,12 +73,20 @@ public class SessionServiceController {
     private static final String QUERY_OPERATOR_SIZE = "$size";
     private static final String QUERY_OPERATOR_AND = "$and";
 
-    @Autowired
     SessionServiceRequestHandler sessionServiceRequestHandler;
 
-    @Autowired
     private ObjectMapper sessionServiceObjectMapper;
 
+    private StudyViewFilterApplier studyViewFilterApplier;
+
+    public SessionServiceController(SessionServiceRequestHandler sessionServiceRequestHandler,
+                                    ObjectMapper sessionServiceObjectMapper,
+                                    StudyViewFilterApplier studyViewFilterApplier) {
+        this.sessionServiceRequestHandler = sessionServiceRequestHandler;
+        this.sessionServiceObjectMapper = sessionServiceObjectMapper;
+        this.studyViewFilterApplier = studyViewFilterApplier;
+    }
+
     @Value("${session.service.url:}")
     private String sessionServiceURL;
 
@@ -211,7 +222,12 @@ public ResponseEntity<Session> getSession(@PathVariable Session.SessionType type
             Session session;
             switch (type) {
                 case virtual_study:
-                    session = sessionServiceObjectMapper.readValue(sessionDataJson, VirtualStudy.class);
+                    VirtualStudy virtualStudy = sessionServiceObjectMapper.readValue(sessionDataJson, VirtualStudy.class);
+                    VirtualStudyData virtualStudyData = virtualStudy.getData();
+                    if (Boolean.TRUE.equals(virtualStudyData.getDynamic())) {
+                        populateVirtualStudySamples(virtualStudyData);
+                    }
+                    session = virtualStudy;
                     break;
                 case settings:
                     session = sessionServiceObjectMapper.readValue(sessionDataJson, PageSettings.class);
@@ -232,6 +248,45 @@ public ResponseEntity<Session> getSession(@PathVariable Session.SessionType type
         }
     }
 
+    /**
+     * This method populates the `virtualStudyData` object with a new set of sample IDs retrieved as the result of executing a query based on virtual study view filters.
+     * It first applies the filters defined within the study view, runs the query to fetch the relevant sample IDs, and then updates the virtualStudyData to reflect these fresh results.
+     * This ensures that the virtual study contains the latest sample IDs.
+     * @param virtualStudyData
+     */
+    private void populateVirtualStudySamples(VirtualStudyData virtualStudyData) {
+        List<SampleIdentifier> sampleIdentifiers = studyViewFilterApplier.apply(virtualStudyData.getStudyViewFilter());
+        Set<VirtualStudySamples> virtualStudySamples = extractVirtualStudySamples(sampleIdentifiers);
+        virtualStudyData.setStudies(virtualStudySamples);
+    }
+
+    /**
+     * Transforms list of sample identifiers to set of virtual study samples
+     * @param sampleIdentifiers
+     */
+    private Set<VirtualStudySamples> extractVirtualStudySamples(List<SampleIdentifier> sampleIdentifiers) {
+        Map<String, Set<String>> sampleIdsByStudyId = groupSampleIdsByStudyId(sampleIdentifiers);
+        return sampleIdsByStudyId.entrySet().stream().map(entry -> {
+            VirtualStudySamples vss = new VirtualStudySamples();
+            vss.setId(entry.getKey());
+            vss.setSamples(entry.getValue());
+            return vss;
+        }).collect(Collectors.toSet());
+    }
+
+    /**
+     * Groups sample IDs by their study ID
+     * @param sampleIdentifiers
+     */
+    private Map<String, Set<String>> groupSampleIdsByStudyId(List<SampleIdentifier> sampleIdentifiers) {
+        return sampleIdentifiers
+            .stream()
+            .collect(
+                Collectors.groupingBy(
+                    SampleIdentifier::getStudyId,
+                    Collectors.mapping(SampleIdentifier::getSampleId, Collectors.toSet())));
+    }
+
     @RequestMapping(value = "/virtual_study", method = RequestMethod.GET)
     @ApiResponse(responseCode = "200", description = "OK",
         content = @Content(array = @ArraySchema(schema = @Schema(implementation = VirtualStudy.class))))

src/main/java/org/cbioportal/web/parameter/VirtualStudyData.java

@@ -24,6 +24,8 @@ public class VirtualStudyData implements Serializable {
     private String typeOfCancerId;
     private String pmid;
 
+    private Boolean dynamic;
+
     public String getOwner() {
         return owner;
     }
@@ -122,4 +124,12 @@ public String getPmid() {
     public void setPmid(String pmid) {
         this.pmid = pmid;
     }
+
+    public Boolean getDynamic() {
+        return dynamic;
+    }
+
+    public void setDynamic(Boolean dynamic) {
+        this.dynamic = dynamic;
+    }
 }

src/test/java/org/cbioportal/web/SessionServiceControllerTest.java

@@ -0,0 +1,92 @@
+package org.cbioportal.web;
+
+import org.cbioportal.service.util.SessionServiceRequestHandler;
+import org.cbioportal.utils.removeme.Session;
+import org.cbioportal.web.config.TestConfig;
+import org.cbioportal.web.parameter.SampleIdentifier;
+import org.cbioportal.web.util.StudyViewFilterApplier;
+import org.hamcrest.Matchers;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.http.MediaType;
+import org.springframework.security.test.context.support.WithMockUser;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.test.web.servlet.MockMvc;
+import org.springframework.test.web.servlet.request.MockMvcRequestBuilders;
+import org.springframework.test.web.servlet.result.MockMvcResultMatchers;
+
+import java.util.List;
+
+@RunWith(SpringJUnit4ClassRunner.class)
+@WebMvcTest
+@ContextConfiguration(classes = {SessionServiceController.class, TestConfig.class})
+public class SessionServiceControllerTest {
+
+    @MockBean
+    SessionServiceRequestHandler sessionServiceRequestHandler;
+
+    @MockBean
+    StudyViewFilterApplier studyViewFilterApplier;
+
+    SampleIdentifier sampleIdentifier1 = new SampleIdentifier();
+    { sampleIdentifier1.setStudyId("STUDY_1"); }
+    SampleIdentifier sampleIdentifier2 = new SampleIdentifier();
+    { sampleIdentifier2.setStudyId("STUDY_2"); }
+
+    @Autowired
+    private MockMvc mockMvc;
+    @Test
+    @WithMockUser
+    public void testStaticVirtualStudy() throws Exception {
+        Mockito.when(sessionServiceRequestHandler.getSessionDataJson(Session.SessionType.virtual_study, "123"))
+            .thenReturn("""
+                {
+                    "id": "123",
+                    "data": {
+                        "name": "Test",
+                        "studies": [
+                            { "id": "STUDY_N", "samples": [ "S1", "S2" ] }
+                        ]
+                    }
+                }
+                """);
+
+        // Should not be used
+        Mockito.when(studyViewFilterApplier.apply(Mockito.any())).thenReturn(List.of(sampleIdentifier1, sampleIdentifier2));
+
+        mockMvc.perform(MockMvcRequestBuilders.get("/api/session/virtual_study/123")
+                .accept(MediaType.APPLICATION_JSON))
+            .andExpect(MockMvcResultMatchers.status().isOk())
+            .andExpect(MockMvcResultMatchers.jsonPath("$.data.studies", Matchers.hasSize(1)))
+            .andExpect(MockMvcResultMatchers.jsonPath("$.data.studies[0].id").value("STUDY_N"));
+        Mockito.verify(studyViewFilterApplier, Mockito.never()).apply(Mockito.any());
+    }
+
+    @Test
+    @WithMockUser 
+    public void testDynamicVirtualStudy() throws Exception {
+        Mockito.when(sessionServiceRequestHandler.getSessionDataJson(Session.SessionType.virtual_study, "123"))
+            .thenReturn("""
+                {
+                    "id": "123",
+                    "data": {
+                        "name": "Test",
+                        "dynamic": true
+                    }
+                }
+                """);
+
+        Mockito.when(studyViewFilterApplier.apply(Mockito.any())).thenReturn(List.of(sampleIdentifier1, sampleIdentifier2));
+
+        mockMvc.perform(MockMvcRequestBuilders.get("/api/session/virtual_study/123")
+                .accept(MediaType.APPLICATION_JSON))
+            .andExpect(MockMvcResultMatchers.status().isOk())
+            .andExpect(MockMvcResultMatchers.jsonPath("$.data.studies", Matchers.hasSize(2)))
+            .andExpect(MockMvcResultMatchers.jsonPath("$.data.studies[*].id").value(Matchers.containsInAnyOrder("STUDY_1", "STUDY_2")));
+    }
+}