Rfc80/treatments patients endpoint (#10903)

* Create new endpoint treatment/patient-counts/fetch * Create StudyViewFilterHelper class * ⬆️ Upgrade CH client Version * Fix Merge Conflict issue * Update Treatment event name * Update to handle patient treatment filtering * Fix sonar issues * Fix sonar comments 2
cBioPortal · Nov 24, 2024 · 94b431c · 94b431c
1 parent 8ab5f25
commit 94b431c
Show file tree

Hide file tree

Showing 15 changed files with 295 additions and 17 deletions.
diff --git a/pom.xml b/pom.xml
@@ -358,7 +358,7 @@
         <dependency>
             <groupId>com.clickhouse</groupId>
             <artifactId>clickhouse-jdbc</artifactId>
-            <version>0.5.0</version>
+            <version>0.6.2</version>
             <!-- use uber jar with all dependencies included, change classifier
             to http for smaller jar -->
             <classifier>all</classifier>

diff --git a/src/main/java/org/cbioportal/model/PatientTreatment.java b/src/main/java/org/cbioportal/model/PatientTreatment.java
@@ -0,0 +1,7 @@
+package org.cbioportal.model;
+
+import java.io.Serializable;
+
+public record PatientTreatment (String treatment, int count) implements Serializable {
+
+}
diff --git a/src/main/java/org/cbioportal/model/PatientTreatmentReport.java b/src/main/java/org/cbioportal/model/PatientTreatmentReport.java
@@ -0,0 +1,11 @@
+package org.cbioportal.model;
+
+import java.io.Serializable;
+import java.util.Collections;
+import java.util.List;
+
+public record PatientTreatmentReport (int totalPatients, int totalSamples, List<PatientTreatment> patientTreatments) implements Serializable {
+    public PatientTreatmentReport(int totalPatients, int totalSamples) {
+        this(totalPatients, totalSamples, Collections.emptyList());
+    } 
+}
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -8,6 +8,8 @@
 import org.cbioportal.model.ClinicalEventTypeCount;
 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.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.StudyViewFilter;
@@ -49,4 +51,8 @@ public interface StudyViewRepository {
     int getSampleProfileCountWithoutPanelData(StudyViewFilter studyViewFilter, String alterationType);
 
     List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter);
+
+    List<PatientTreatment> getPatientTreatments(StudyViewFilter studyViewFilter);
+
+    PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter);
 }
diff --git a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
@@ -0,0 +1,78 @@
+package org.cbioportal.persistence.helper;
+
+import org.cbioportal.model.ClinicalAttribute;
+import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
+import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
+import org.cbioportal.web.parameter.StudyViewFilter;
+import org.springframework.lang.NonNull;
+import org.springframework.lang.Nullable;
+
+import java.util.EnumMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+
+public class StudyViewFilterHelper {
+    public static StudyViewFilterHelper build(@Nullable StudyViewFilter studyViewFilter, @Nullable EnumMap<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap) {
+        if (Objects.isNull(studyViewFilter)) {
+            studyViewFilter = new StudyViewFilter();
+        }
+        if (Objects.isNull(clinicalAttributesMap)) {
+            clinicalAttributesMap = new EnumMap<>(ClinicalAttributeDataSource.class);
+        }
+        return new StudyViewFilterHelper(studyViewFilter, clinicalAttributesMap);
+    }
+
+    private final StudyViewFilter studyViewFilter;
+    private final CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter;
+
+
+    private StudyViewFilterHelper(@NonNull StudyViewFilter studyViewFilter, @NonNull Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap ) {
+        this.studyViewFilter = studyViewFilter;
+        this.categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter, clinicalAttributesMap);
+    }
+
+    private CategorizedClinicalDataCountFilter extractClinicalDataCountFilters(final StudyViewFilter studyViewFilter, Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> clinicalAttributesMap) {
+
+        if (studyViewFilter.getClinicalDataFilters() == null || clinicalAttributesMap.isEmpty()) {
+            return CategorizedClinicalDataCountFilter.getBuilder().build();
+        }
+
+        List<String> patientCategoricalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.PATIENT)
+            .stream().filter(ca -> ca.getDatatype().equals("STRING"))
+            .map(ClinicalAttribute::getAttrId)
+            .toList();
+
+        List<String> patientNumericalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.PATIENT)
+            .stream().filter(ca -> ca.getDatatype().equals("NUMBER"))
+            .map(ClinicalAttribute::getAttrId)
+            .toList();
+
+        List<String> sampleCategoricalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.SAMPLE)
+            .stream().filter(ca -> ca.getDatatype().equals("STRING"))
+            .map(ClinicalAttribute::getAttrId)
+            .toList();
+
+        List<String> sampleNumericalAttributes = clinicalAttributesMap.get(ClinicalAttributeDataSource.SAMPLE)
+            .stream().filter(ca -> ca.getDatatype().equals("NUMBER"))
+            .map(ClinicalAttribute::getAttrId)
+            .toList();
+
+        return CategorizedClinicalDataCountFilter.getBuilder()
+            .setPatientCategoricalClinicalDataFilters(studyViewFilter.getClinicalDataFilters()
+                .stream().filter(clinicalDataFilter -> patientCategoricalAttributes.contains(clinicalDataFilter.getAttributeId()))
+                .toList())
+            .setPatientNumericalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream()
+                .filter(clinicalDataFilter -> patientNumericalAttributes.contains(clinicalDataFilter.getAttributeId()))
+                .toList())
+            .setSampleCategoricalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream()
+                .filter(clinicalDataFilter -> sampleCategoricalAttributes.contains(clinicalDataFilter.getAttributeId()))
+                .toList())
+            .setSampleNumericalClinicalDataFilters(studyViewFilter.getClinicalDataFilters().stream()
+                .filter(clinicalDataFilter -> sampleNumericalAttributes.contains(clinicalDataFilter.getAttributeId()))
+                .toList())
+            .build();
+    }
+
+
+}
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -10,6 +10,8 @@
 import org.cbioportal.model.CopyNumberCountByGene;
 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.persistence.helper.AlterationFilterHelper;
 import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
@@ -55,4 +57,7 @@ List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, C
     int getSampleProfileCountWithoutPanelData(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
 
     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);
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -8,6 +8,8 @@
 import org.cbioportal.model.GenePanelToGene;
 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.persistence.StudyViewRepository;
 import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
@@ -114,8 +116,9 @@ public List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFi
 
 
     private boolean shouldApplyPatientIdFilters(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
-        return studyViewFilter.getClinicalEventFilters() != null && !studyViewFilter.getClinicalEventFilters().isEmpty() 
-        || categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters() != null && !categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters().isEmpty()
+        return studyViewFilter.getClinicalEventFilters() != null && !studyViewFilter.getClinicalEventFilters().isEmpty()
+            || studyViewFilter.getPatientTreatmentFilters() != null && studyViewFilter.getPatientTreatmentFilters().getFilters()!= null && !studyViewFilter.getPatientTreatmentFilters().getFilters().isEmpty()
+            || categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters() != null && !categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters().isEmpty()
             || categorizedClinicalDataCountFilter.getPatientNumericalClinicalDataFilters() != null && !categorizedClinicalDataCountFilter.getPatientNumericalClinicalDataFilters().isEmpty();
     }
 
@@ -180,12 +183,35 @@ public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter s
             shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter));
     }
 
+    @Override
+    public List<PatientTreatment> getPatientTreatments(StudyViewFilter studyViewFilter) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
+        return mapper.getPatientTreatments(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(studyViewFilter, categorizedClinicalDataCountFilter));
+    }
+
+    @Override
+    public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
+        var patientTreatmentCounts = mapper.getPatientTreatmentCounts(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() {
         clinicalAttributesMap = this.getClinicalAttributes()
             .stream()
             .collect(Collectors.groupingBy(ca -> ca.getPatientAttribute() ? ClinicalAttributeDataSource.PATIENT : ClinicalAttributeDataSource.SAMPLE));
     }
 
+    private Map<ClinicalAttributeDataSource, List<ClinicalAttribute>> getClinicalAttributeNameMap() {
+        if (clinicalAttributesMap.isEmpty()) {
+            buildClinicalAttributeNameMap();
+        }
+        return clinicalAttributesMap;
+    }
+
     private CategorizedClinicalDataCountFilter extractClinicalDataCountFilters(final StudyViewFilter studyViewFilter) {
         if (clinicalAttributesMap.isEmpty()) {
             buildClinicalAttributeNameMap();

diff --git a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java b/src/main/java/org/cbioportal/service/StudyViewColumnarService.java
@@ -7,6 +7,7 @@
 import org.cbioportal.model.ClinicalEventTypeCount;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.CopyNumberCountByGene;
+import org.cbioportal.model.PatientTreatmentReport;
 import org.cbioportal.model.Sample;
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.StudyViewFilter;
@@ -35,5 +36,5 @@ public interface StudyViewColumnarService {
     List<GenomicDataCount> getGenomicDataCounts(StudyViewFilter studyViewFilter);
 
     List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter);
-
+    PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter);
 }
diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -8,6 +8,7 @@
 import org.cbioportal.model.ClinicalEventTypeCount;
 import org.cbioportal.model.CopyNumberCountByGene;
 import org.cbioportal.model.GenomicDataCount;
+import org.cbioportal.model.PatientTreatmentReport;
 import org.cbioportal.model.Sample;
 import org.cbioportal.persistence.StudyViewRepository;
 import org.cbioportal.service.AlterationCountService;
@@ -57,6 +58,11 @@ public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter s
         return studyViewRepository.getClinicalEventTypeCounts(studyViewFilter);
     }
 
+    @Override
+    public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter) {
+        return studyViewRepository.getPatientTreatmentReport(studyViewFilter);
+    }
+
     public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter) {
         return alterationCountService.getCnaGenes(studyViewFilter);
     }

diff --git a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java b/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
@@ -13,11 +13,14 @@
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataBin;
 import org.cbioportal.model.ClinicalDataCountItem;
+import org.cbioportal.model.ClinicalEventKeyCode;
 import org.cbioportal.model.ClinicalEventTypeCount;
 import org.cbioportal.model.ClinicalViolinPlotData;
 import org.cbioportal.model.CopyNumberCountByGene;
 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.service.ClinicalDataDensityPlotService;
 import org.cbioportal.service.StudyViewColumnarService;
@@ -350,4 +353,33 @@ public ResponseEntity<List<ClinicalEventTypeCount>> getClinicalEventTypeCounts(
     ) {
         return new ResponseEntity<>(studyViewColumnarService.getClinicalEventTypeCounts(interceptedStudyViewFilter), HttpStatus.OK);
     }
+
+    @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
+    @PostMapping(value = "/column-store/treatments/patient-counts/fetch", produces = MediaType.APPLICATION_JSON_VALUE)
+    @Operation(description = "Get all patient level treatments")
+    @ApiResponse(responseCode = "200", description = "OK",
+        content = @Content(array = @ArraySchema(schema = @Schema(implementation = PatientTreatmentRow.class))))
+    public ResponseEntity<PatientTreatmentReport> getPatientTreatmentCounts(
+        @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.getPatientTreatmentReport(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
@@ -134,6 +134,7 @@ public class InvolvedCancerStudyExtractorInterceptor implements HandlerIntercept
     public static final String CLINICAL_EVENT_TYPE_COUNT_FETCH_PATH = "/clinical-event-type-counts/fetch";
     public static final String SURVIVAL_DATA_FETCH_PATH = "/survival-data/fetch";
     public static final String CLINICAL_EVENT_META_FETCH_PATH = "/clinical-events-meta/fetch";
+    public static final String TREATMENTS_PATIENT_COUNT_FETCH_PATH = "/treatments/patient-counts/fetch";
 
     @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) {
         if (!request.getMethod().equals("POST")) {
@@ -178,7 +179,8 @@ public class InvolvedCancerStudyExtractorInterceptor implements HandlerIntercept
         } else if (Arrays.asList(STUDY_VIEW_CLINICAL_DATA_DENSITY_PATH, STUDY_VIEW_CLINICAL_DATA_VIOLIN_PATH, STUDY_VIEW_CNA_GENES, 
                 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_PATH, TREATMENTS_SAMPLE_PATH, STUDY_VIEW_PROFILE_SAMPLE_COUNTS_PATH, CLINICAL_EVENT_TYPE_COUNT_FETCH_PATH,
+            TREATMENTS_PATIENT_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
@@ -122,6 +122,22 @@
             </where>
         </foreach>
     </sql>
+
+    <sql id="applyPatientTreatmentFilter">
+        <foreach item="andedPatientTreatmentFilters" collection="studyViewFilter.getPatientTreatmentFilters().getFilters()" open="INTERSECT"
+                 separator="INTERSECT">
+            SELECT patient_unique_id
+            FROM clinical_event_derived
+            <where>
+                <foreach item="patientTreatmentFilter" collection="andedPatientTreatmentFilters.getFilters()" open="(" separator=") OR ("
+                         close=")">
+                    event_type = 'Treatment'
+                    AND key = 'AGENT'
+                    AND value = '${patientTreatmentFilter.treatment}'
+                </foreach>
+            </where>
+        </foreach> 
+    </sql>
 
     <sql id="patientUniqueIdsFromStudyViewFilter">
         <trim prefixOverrides="INTERSECT">
@@ -144,9 +160,13 @@
                 </foreach>
             </if>
             <!-- Clinical Event Filter -->
-            <if test="studyViewFilter.clinicalEventFilters != null and !studyViewFilter.clinicalEventFilters.isEmpty()">
+            <if test="studyViewFilter.getClinicalEventFilters() != null and !studyViewFilter.getClinicalEventFilters().isEmpty()">
                 <include refid="applyClinicalEventTypeFilter"/>
             </if>
+            <!-- Patient Treatment Filter -->
+            <if test="studyViewFilter.getPatientTreatmentFilters() != null and !studyViewFilter.getPatientTreatmentFilters().getFilters().isEmpty()">
+                <include refid="applyPatientTreatmentFilter"/>
+            </if>
         </trim>
     </sql>