Rfc80/update open api annotation for sampleTreatment Endpoint (#10929)

* Fix Sample Treatment Endpoint * Fix Sample ID only StudyView Filter
cBioPortal · Aug 6, 2024 · d62c6e5 · d62c6e5
1 parent bf71f1b
commit d62c6e5
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Showing 4 changed files with 20 additions and 10 deletions.
diff --git a/src/main/java/org/cbioportal/model/SampleTreatmentReport.java b/src/main/java/org/cbioportal/model/SampleTreatmentReport.java
@@ -2,5 +2,5 @@
 
 import java.util.Collection;
 
-public record SampleTreatmentReport(int totalSampleCount, Collection<SampleTreatment> treatments) {
+public record SampleTreatmentReport(int totalSamples, Collection<SampleTreatmentRow> treatments) {
 }
diff --git a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java b/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java
@@ -2,11 +2,16 @@
 
 import org.cbioportal.model.PatientTreatmentReport;
 import org.cbioportal.model.SampleTreatmentReport;
+import org.cbioportal.model.SampleTreatmentRow;
+import org.cbioportal.model.TemporalRelation;
 import org.cbioportal.persistence.StudyViewRepository;
 import org.cbioportal.web.parameter.StudyViewFilter;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
+import java.util.Set;
+import java.util.stream.Stream;
+
 @Service
 public class TreatmentCountReportServiceImpl implements TreatmentCountReportService {
 
@@ -26,7 +31,13 @@ public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyVie
 
     @Override
     public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter) {
-        var sampleTreatments = studyViewRepository.getSampleTreatments(studyViewFilter);
+        var sampleTreatments = studyViewRepository.getSampleTreatments(studyViewFilter)
+            .stream()
+            .flatMap(sampleTreatment -> 
+                Stream.of(new SampleTreatmentRow(TemporalRelation.Pre, sampleTreatment.treatment(), sampleTreatment.preSampleCount(), Set.of()),
+                    new SampleTreatmentRow(TemporalRelation.Post, sampleTreatment.treatment(), sampleTreatment.postSampleCount(), Set.of() ))
+                    )
+            .toList();
         var totalSampleTreatmentCount = studyViewRepository.getTotalSampleTreatmentCount(studyViewFilter);
         return new SampleTreatmentReport(totalSampleTreatmentCount, sampleTreatments);
     }

diff --git a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java b/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
@@ -21,7 +21,6 @@
 import org.cbioportal.model.DensityPlotData;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.PatientTreatmentReport;
-import org.cbioportal.model.PatientTreatmentRow;
 import org.cbioportal.model.Sample;
 import org.cbioportal.model.SampleTreatmentReport;
 import org.cbioportal.service.ClinicalDataDensityPlotService;
@@ -397,8 +396,8 @@ public ResponseEntity<PatientTreatmentReport> fetchPatientTreatmentCounts(
     @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
     @PostMapping(value = "/column-store/treatments/sample-counts/fetch", produces = MediaType.APPLICATION_JSON_VALUE)
     @ApiResponse(responseCode = "200", description = "OK",
-        content = @Content(array = @ArraySchema(schema = @Schema(implementation = PatientTreatmentRow.class))))
-    public ResponseEntity<SampleTreatmentReport> getSampleTreatmentCounts(
+        content = @Content(schema = @Schema(implementation = SampleTreatmentReport.class)))
+    public ResponseEntity<SampleTreatmentReport> fetchSampleTreatmentCounts(
         @Parameter(required = false )
         @RequestParam(name = "tier", required = false, defaultValue = "Agent")
         ClinicalEventKeyCode tier,

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -502,11 +502,11 @@
     </sql>
 
     <sql id="applyStudyViewFilterUsingSampleId">
-        sample_unique_id IN ( <include refid="sampleUniqueIdsFromStudyViewFilter"/>)
-        <if test="applyPatientIdFilters == true">
-            INTERSECT
-            <include refid="getSampleIdsFromPatientIds"/>
-        </if> 
+        sample_unique_id IN (<include refid="sampleUniqueIdsFromStudyViewFilter"/>
+            <if test="applyPatientIdFilters == true">
+                INTERSECT <include refid="getSampleIdsFromPatientIds"/>
+            </if>
+        )
     </sql>
 
     <sql id="getSampleIdsFromPatientIds">