Rfc80/sample treatment endpoint (#10927)

* Add Sample Count Report Endpoint * Push counting logic to sql * Remove unused methods * Update PatientTreatments to pass int from db for totalPatientTreatmentCount * Fix tests * Add unit test for sample Treatments * Remove unused import * Fix indentation
cBioPortal · Aug 5, 2024 · bf71f1b · bf71f1b
1 parent e935c41
commit bf71f1b
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Showing 17 changed files with 322 additions and 37 deletions.
diff --git a/src/main/java/org/cbioportal/model/SampleTreatment.java b/src/main/java/org/cbioportal/model/SampleTreatment.java
@@ -0,0 +1,4 @@
+package org.cbioportal.model;
+
+public record SampleTreatment(String treatment, int preSampleCount, int postSampleCount) {
+}
diff --git a/src/main/java/org/cbioportal/model/SampleTreatmentReport.java b/src/main/java/org/cbioportal/model/SampleTreatmentReport.java
@@ -0,0 +1,6 @@
+package org.cbioportal.model;
+
+import java.util.Collection;
+
+public record SampleTreatmentReport(int totalSampleCount, Collection<SampleTreatment> treatments) {
+}
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -9,8 +9,8 @@
 import org.cbioportal.model.CopyNumberCountByGene;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.PatientTreatment;
-import org.cbioportal.model.PatientTreatmentReport;
 import org.cbioportal.model.Sample;
+import org.cbioportal.model.SampleTreatment;
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.StudyViewFilter;
 
@@ -53,6 +53,10 @@ public interface StudyViewRepository {
     List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter);
 
     List<PatientTreatment> getPatientTreatments(StudyViewFilter studyViewFilter);
+
+    int getTotalPatientTreatmentCount(StudyViewFilter studyViewFilter);
 
-    PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter);
+    List<SampleTreatment> getSampleTreatments(StudyViewFilter studyViewFilter);
+
+    int getTotalSampleTreatmentCount(StudyViewFilter studyViewFilter);
 }
diff --git a/src/main/java/org/cbioportal/persistence/model/SampleAcquisitionEventRecord.java b/src/main/java/org/cbioportal/persistence/model/SampleAcquisitionEventRecord.java
@@ -0,0 +1,4 @@
+package org.cbioportal.persistence.model;
+
+public record SampleAcquisitionEventRecord(String sampleId, String patientUniqueId, String cancerStudyId, int timeTaken) {
+}
diff --git a/src/main/java/org/cbioportal/persistence/model/TreatmentRecord.java b/src/main/java/org/cbioportal/persistence/model/TreatmentRecord.java
@@ -0,0 +1,4 @@
+package org.cbioportal.persistence.model;
+
+public record TreatmentRecord(String patientUniqueId, String treatment, int startTime, int stopTime) {
+}
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -1,6 +1,5 @@
 package org.cbioportal.persistence.mybatisclickhouse;
 
-import org.apache.ibatis.annotations.MapKey;
 import org.cbioportal.model.AlterationCountByGene;
 import org.cbioportal.model.CaseListDataCount;
 import org.cbioportal.model.ClinicalAttribute;
@@ -11,14 +10,13 @@
 import org.cbioportal.model.GenePanelToGene;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.PatientTreatment;
-import org.cbioportal.model.PatientTreatmentReport;
 import org.cbioportal.model.Sample;
+import org.cbioportal.model.SampleTreatment;
 import org.cbioportal.persistence.helper.AlterationFilterHelper;
 import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
 
 import java.util.List;
-import java.util.Map;
 
 
 public interface StudyViewMapper {
@@ -59,5 +57,7 @@ List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, C
     List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
 
     List<PatientTreatment> getPatientTreatments(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
-    PatientTreatmentReport getPatientTreatmentCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
+    int getPatientTreatmentCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
+    List<SampleTreatment> getSampleTreatmentCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
+    int getTotalSampleTreatmentCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -9,8 +9,8 @@
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.CopyNumberCountByGene;
 import org.cbioportal.model.PatientTreatment;
-import org.cbioportal.model.PatientTreatmentReport;
 import org.cbioportal.model.Sample;
+import org.cbioportal.model.SampleTreatment;
 import org.cbioportal.persistence.StudyViewRepository;
 import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
 import org.cbioportal.persistence.helper.AlterationFilterHelper;
@@ -190,13 +190,24 @@ public List<PatientTreatment> getPatientTreatments(StudyViewFilter studyViewFilt
     }
 
     @Override
-    public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter) {
+    public int getTotalPatientTreatmentCount(StudyViewFilter studyViewFilter) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
-        var patientTreatmentCounts = mapper.getPatientTreatmentCounts(studyViewFilter, categorizedClinicalDataCountFilter, 
+       return mapper.getPatientTreatmentCounts(studyViewFilter, categorizedClinicalDataCountFilter, 
+            shouldApplyPatientIdFilters(studyViewFilter, categorizedClinicalDataCountFilter));
+    }
+
+    @Override
+    public List<SampleTreatment> getSampleTreatments(StudyViewFilter studyViewFilter) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
+        return mapper.getSampleTreatmentCounts(studyViewFilter, categorizedClinicalDataCountFilter,
+            shouldApplyPatientIdFilters(studyViewFilter, categorizedClinicalDataCountFilter));
+    }
+
+    @Override
+    public int getTotalSampleTreatmentCount(StudyViewFilter studyViewFilter) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
+        return mapper.getTotalSampleTreatmentCounts(studyViewFilter, categorizedClinicalDataCountFilter,
             shouldApplyPatientIdFilters(studyViewFilter, categorizedClinicalDataCountFilter));
-        var patientTreatments = mapper.getPatientTreatments(studyViewFilter, categorizedClinicalDataCountFilter, 
-            shouldApplyPatientIdFilters(studyViewFilter, categorizedClinicalDataCountFilter)); 
-        return new PatientTreatmentReport(patientTreatmentCounts.totalPatients(), patientTreatmentCounts.totalSamples(), patientTreatments);
     }
 
     private void buildClinicalAttributeNameMap() {

diff --git a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java b/src/main/java/org/cbioportal/service/StudyViewColumnarService.java
@@ -9,6 +9,7 @@
 import org.cbioportal.model.CopyNumberCountByGene;
 import org.cbioportal.model.PatientTreatmentReport;
 import org.cbioportal.model.Sample;
+import org.cbioportal.model.SampleTreatmentReport;
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.StudyViewFilter;
 
@@ -37,4 +38,5 @@ public interface StudyViewColumnarService {
 
     List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter);
     PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter);
+    SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter);
 }
diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -10,9 +10,11 @@
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.PatientTreatmentReport;
 import org.cbioportal.model.Sample;
+import org.cbioportal.model.SampleTreatmentReport;
 import org.cbioportal.persistence.StudyViewRepository;
 import org.cbioportal.service.AlterationCountService;
 import org.cbioportal.service.StudyViewColumnarService;
+import org.cbioportal.service.treatment.TreatmentCountReportService;
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.StudyViewFilter;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -30,11 +32,15 @@ public class StudyViewColumnarServiceImpl implements StudyViewColumnarService {
     private final StudyViewRepository studyViewRepository;
 
     private final AlterationCountService alterationCountService;
+    private final TreatmentCountReportService treatmentCountReportService;
 
     @Autowired
-    public StudyViewColumnarServiceImpl(StudyViewRepository studyViewRepository, AlterationCountService alterationCountService) {
+    public StudyViewColumnarServiceImpl(StudyViewRepository studyViewRepository, 
+                                        AlterationCountService alterationCountService,
+                                        TreatmentCountReportService treatmentCountReportService) {
         this.studyViewRepository = studyViewRepository;
         this.alterationCountService = alterationCountService;
+        this.treatmentCountReportService = treatmentCountReportService;
     }
 
     @Cacheable(cacheResolver = "generalRepositoryCacheResolver", condition = "@cacheEnabledConfig.getEnabled()")
@@ -60,7 +66,12 @@ public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter s
 
     @Override
     public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter) {
-        return studyViewRepository.getPatientTreatmentReport(studyViewFilter);
+        return treatmentCountReportService.getPatientTreatmentReport(studyViewFilter);
+    }
+
+    @Override
+    public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter) {
+        return treatmentCountReportService.getSampleTreatmentReport(studyViewFilter);
     }
 
     public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter) {

diff --git a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java b/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java
@@ -0,0 +1,10 @@
+package org.cbioportal.service.treatment;
+
+import org.cbioportal.model.PatientTreatmentReport;
+import org.cbioportal.model.SampleTreatmentReport;
+import org.cbioportal.web.parameter.StudyViewFilter;
+
+public interface TreatmentCountReportService {
+    PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter);
+    SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter);
+}
diff --git a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java b/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java
@@ -0,0 +1,34 @@
+package org.cbioportal.service.treatment;
+
+import org.cbioportal.model.PatientTreatmentReport;
+import org.cbioportal.model.SampleTreatmentReport;
+import org.cbioportal.persistence.StudyViewRepository;
+import org.cbioportal.web.parameter.StudyViewFilter;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+@Service
+public class TreatmentCountReportServiceImpl implements TreatmentCountReportService {
+
+    private final StudyViewRepository studyViewRepository;
+
+    @Autowired
+    public TreatmentCountReportServiceImpl(StudyViewRepository studyViewRepository) {
+        this.studyViewRepository = studyViewRepository;
+    }
+
+    @Override
+    public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter) {
+        var patientTreatments = studyViewRepository.getPatientTreatments(studyViewFilter);
+        var totalPatientTreatmentCount = studyViewRepository.getTotalPatientTreatmentCount(studyViewFilter);
+        return new PatientTreatmentReport(totalPatientTreatmentCount, 0, patientTreatments);
+    }
+
+    @Override
+    public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter) {
+        var sampleTreatments = studyViewRepository.getSampleTreatments(studyViewFilter);
+        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
@@ -23,6 +23,7 @@
 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;
 import org.cbioportal.service.StudyViewColumnarService;
 import org.cbioportal.service.ViolinPlotService;
@@ -393,4 +394,31 @@ public ResponseEntity<PatientTreatmentReport> fetchPatientTreatmentCounts(
             HttpStatus.OK);
     }
 
+    @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(
+        @Parameter(required = false )
+        @RequestParam(name = "tier", required = false, defaultValue = "Agent")
+        ClinicalEventKeyCode tier,
+
+        @Parameter(required = true, description = "Study view filter")
+        @Valid
+        @RequestBody(required = false)
+        StudyViewFilter studyViewFilter,
+
+        @Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface
+        @RequestAttribute(required = false, value = "involvedCancerStudies")
+        Collection<String> involvedCancerStudies,
+
+        @Parameter(hidden = true) // 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<>(studyViewColumnarService.getSampleTreatmentReport(interceptedStudyViewFilter),
+            HttpStatus.OK);
+    }
+
 }
diff --git a/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java b/src/main/java/org/cbioportal/web/util/InvolvedCancerStudyExtractorInterceptor.java
@@ -133,6 +133,7 @@ public class InvolvedCancerStudyExtractorInterceptor implements HandlerIntercept
     public static final String GENERIC_ASSAY_BINARY_ENRICHMENT_FETCH_PATH = "/generic-assay-binary-enrichments/fetch";
     public static final String CLINICAL_EVENT_TYPE_COUNT_FETCH_PATH = "/clinical-event-type-counts/fetch";
     public static final String TREATMENTS_PATIENT_COUNT_FETCH_PATH = "/treatments/patient-counts/fetch";
+    public static final String TREATMENTS_SAMPLE_COUNT_FETCH_PATH = "/treatments/sample-counts/fetch";
 
     @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) {
         if (!request.getMethod().equals("POST")) {
@@ -178,7 +179,7 @@ public class InvolvedCancerStudyExtractorInterceptor implements HandlerIntercept
                 STUDY_VIEW_FILTERED_SAMPLES, STUDY_VIEW_MUTATED_GENES, STUDY_VIEW_STRUCTURAL_VARIANT_GENES,
                 STUDY_VIEW_STRUCTURAL_VARIANT_COUNTS, STUDY_VIEW_SAMPLE_COUNTS, STUDY_VIEW_SAMPLE_LIST_COUNTS_PATH, STUDY_VIEW_CLINICAL_TABLE_DATA_FETCH_PATH,
                 TREATMENTS_PATIENT_PATH, TREATMENTS_SAMPLE_PATH, STUDY_VIEW_PROFILE_SAMPLE_COUNTS_PATH, CLINICAL_EVENT_TYPE_COUNT_FETCH_PATH,
-            TREATMENTS_PATIENT_COUNT_FETCH_PATH
+            TREATMENTS_PATIENT_COUNT_FETCH_PATH, TREATMENTS_SAMPLE_COUNT_FETCH_PATH
         ).contains(requestPathInfo)) {
             return extractAttributesFromStudyViewFilter(request);
         } else if (requestPathInfo.equals(CLINICAL_DATA_ENRICHMENT_FETCH_PATH)) {

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
@@ -106,9 +106,57 @@
                 </foreach>
             </if>
             <!-- ... extend for other elements of the StudyViewFilter object -->
+            <!-- Apply Sample Treatment Filter -->
+            <if test="studyViewFilter.sampleTreatmentFilters != null and !studyViewFilter.sampleTreatmentFilters.getFilters().isEmpty()">
+                <include refid="applySampleTreatmentFilter"/>
+            </if>
         </trim>
     </sql>
-
+
+    <sql id="applySampleTreatmentFilter">
+        <foreach item="andedSampleTreatmentFilters" collection="studyViewFilter.sampleTreatmentFilters.getFilters()" open="INTERSECT" separator="INTERSECT">
+            SELECT  concat(ced.cancer_study_identifier, '_', ced.sample_id) AS sample_unique_id
+            FROM (
+            <!-- Nested sub query to grab minimum sample acquisition event -->
+                SELECT
+                    ced.value AS sample_id,
+                    ced.patient_unique_id AS patient_unique_id,
+                    min(ced.start_date) AS time_taken,
+                    ced.cancer_study_identifier AS cancer_study_identifier
+                    FROM clinical_event_derived ced
+                    <where>
+                        key = 'SAMPLE_ID'
+                        AND (event_type LIKE 'Sample Acquisition' OR event_type LIKE 'SPECIMEN')
+                    </where>
+                    GROUP BY patient_unique_id, ced.value, cancer_study_identifier 
+            ) ced
+            INNER JOIN (
+            <!-- Nested sub query to grab all treatments group by patients-->
+                SELECT
+                    patient_unique_id,
+                    value AS treatment,
+                    argMin(start_date, start_date) AS treatment_time_taken
+                FROM clinical_event_derived
+                WHERE event_type = 'Treatment'
+                AND key = 'AGENT'
+                GROUP BY patient_unique_id, value
+            ) ced_inner ON ced_inner.patient_unique_id = ced.patient_unique_id
+            <where>
+                <foreach item="sampleTreatmentFilter" collection="andedSampleTreatmentFilters.getFilters()" open="AND ((" separator=") OR (" close="))">
+                    ced_inner.treatment = '${sampleTreatmentFilter.treatment}'
+                    <choose>
+                        <when test="sampleTreatmentFilter.time.name() == 'Pre'">
+                            AND ced.time_taken &lt;=  ced_inner.treatment_time_taken 
+                        </when>
+                        <otherwise>
+                            AND ced.time_taken &gt; ced_inner.treatment_time_taken 
+                        </otherwise>
+                    </choose>
+                </foreach>
+            </where>
+            GROUP BY patient_unique_id, ced.sample_id, ced.time_taken, ced.cancer_study_identifier, ced_inner.treatment, ced_inner.treatment_time_taken
+        </foreach>
+    </sql>
     <sql id="applyClinicalEventTypeFilter">
         <foreach item="clinicalEventFilter" collection="studyViewFilter.getClinicalEventFilters()" open="INTERSECT"
                  separator="INTERSECT">