From be8648cbb6a8d06d10a8402cff8be3f3c52876ac Mon Sep 17 00:00:00 2001
From: Ruslan Forostianov <ruslan@se4.bio>
Date: Wed, 2 Oct 2024 21:15:52 +0200
Subject: [PATCH] Query sample IDs using Virtual Study View Filters is it's of
 dynamic type

---
 .../web/SessionServiceController.java         | 37 ++++++++++++++++++-
 1 file changed, 36 insertions(+), 1 deletion(-)

diff --git a/src/main/java/org/cbioportal/web/SessionServiceController.java b/src/main/java/org/cbioportal/web/SessionServiceController.java
index 83cf95c932a..286f8d9aa8b 100644
--- a/src/main/java/org/cbioportal/web/SessionServiceController.java
+++ b/src/main/java/org/cbioportal/web/SessionServiceController.java
@@ -23,10 +23,13 @@
 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;
@@ -57,6 +60,7 @@
 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;
 
@@ -76,6 +80,9 @@ public class SessionServiceController {
     @Autowired
     private ObjectMapper sessionServiceObjectMapper;
 
+    @Autowired
+    private StudyViewFilterApplier studyViewFilterApplier;
+
     @Value("${session.service.url:}")
     private String sessionServiceURL;
 
@@ -211,7 +218,12 @@ 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 +244,29 @@ 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());
+        Map<String, Set<String>> sampleIdsByStudyId = sampleIdentifiers
+            .stream()
+            .collect(
+                Collectors.groupingBy(
+                    SampleIdentifier::getStudyId,
+                    Collectors.mapping(SampleIdentifier::getSampleId, Collectors.toSet())));
+        Set<VirtualStudySamples> virtualStudySamples = sampleIdsByStudyId.entrySet().stream().map(entry -> {
+            VirtualStudySamples vss = new VirtualStudySamples();
+            vss.setId(entry.getKey());
+            vss.setSamples(entry.getValue());
+            return vss;
+        }).collect(Collectors.toSet());
+        virtualStudyData.setStudies(virtualStudySamples);
+    }
+
     @RequestMapping(value = "/virtual_study", method = RequestMethod.GET)
     @ApiResponse(responseCode = "200", description = "OK",
         content = @Content(array = @ArraySchema(schema = @Schema(implementation = VirtualStudy.class))))