cBioPortal · alisman · Oct 9, 2024 · Oct 9, 2024 · Oct 9, 2024 · Oct 9, 2024
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -7,6 +7,7 @@
 import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.ClinicalEventTypeCount;
 import org.cbioportal.model.CopyNumberCountByGene;
+import org.cbioportal.model.GenericAssayDataCountItem;
 import org.cbioportal.model.GenomicDataCountItem;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.MolecularProfile;
@@ -16,6 +17,7 @@
 import org.cbioportal.model.StudyViewFilterContext;
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.GenericAssayDataBinFilter;
+import org.cbioportal.web.parameter.GenericAssayDataFilter;
 import org.cbioportal.web.parameter.GenomicDataBinFilter;
 import org.cbioportal.web.parameter.GenomicDataFilter;
 
@@ -68,6 +70,8 @@ public interface StudyViewRepository {
     int getTotalSampleTreatmentCount(StudyViewFilterContext studyViewFilterContext);
 
     List<GenomicDataCountItem> getCNACounts(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters);
+
+    List<GenericAssayDataCountItem> getGenericAssayDataCounts(StudyViewFilterContext studyViewFilterContext, List<GenericAssayDataFilter> genericAssayDataFilters);
 
     Map<String, Integer> getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter);
 

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -9,6 +9,7 @@
 import org.cbioportal.model.ClinicalEventTypeCount;
 import org.cbioportal.model.CopyNumberCountByGene;
 import org.cbioportal.model.GenePanelToGene;
+import org.cbioportal.model.GenericAssayDataCountItem;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.GenomicDataCountItem;
 import org.cbioportal.model.PatientTreatment;
@@ -18,6 +19,7 @@
 import org.cbioportal.persistence.helper.AlterationFilterHelper;
 import org.cbioportal.persistence.helper.StudyViewFilterHelper;
 import org.cbioportal.web.parameter.GenericAssayDataBinFilter;
+import org.cbioportal.web.parameter.GenericAssayDataFilter;
 import org.cbioportal.web.parameter.GenomicDataBinFilter;
 import org.cbioportal.web.parameter.GenomicDataFilter;
 
@@ -66,6 +68,8 @@ public interface StudyViewMapper {
     int getTotalSampleTreatmentCounts(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
 
     List<GenomicDataCountItem> getCNACounts(StudyViewFilterHelper studyViewFilterHelper, List<GenomicDataFilter> genomicDataFilters);
+
+    List<GenericAssayDataCountItem> getGenericAssayDataCounts(StudyViewFilterHelper studyViewFilterHelper, List<GenericAssayDataFilter> genericAssayDataFilters);
 
     Map<String, Integer> getMutationCounts(StudyViewFilterHelper studyViewFilterHelper, GenomicDataFilter genomicDataFilter);
 

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -6,6 +6,7 @@
 import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.ClinicalEventTypeCount;
 import org.cbioportal.model.GenePanelToGene;
+import org.cbioportal.model.GenericAssayDataCountItem;
 import org.cbioportal.model.GenomicDataCountItem;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.CopyNumberCountByGene;
@@ -20,6 +21,7 @@
 import org.cbioportal.persistence.helper.StudyViewFilterHelper;
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.GenericAssayDataBinFilter;
+import org.cbioportal.web.parameter.GenericAssayDataFilter;
 import org.cbioportal.web.parameter.GenomicDataBinFilter;
 import org.cbioportal.web.parameter.GenomicDataFilter;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -245,17 +247,19 @@ private Map<DataSource, List<MolecularProfile>> getGenericAssayProfilesMap() {
 
     @Override
     public List<GenomicDataCountItem> getCNACounts(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters) {
-
         return mapper.getCNACounts(createStudyViewFilterHelper(studyViewFilterContext), genomicDataFilters);
     }
 
-    public Map<String, Integer> getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter) {
+    @Override
+    public List<GenericAssayDataCountItem> getGenericAssayDataCounts(StudyViewFilterContext studyViewFilterContext, List<GenericAssayDataFilter> genericAssayDataFilters) {
+        return mapper.getGenericAssayDataCounts(createStudyViewFilterHelper(studyViewFilterContext), genericAssayDataFilters);
+    }
 
+    public Map<String, Integer> getMutationCounts(StudyViewFilterContext studyViewFilterContext, GenomicDataFilter genomicDataFilter) {
         return mapper.getMutationCounts(createStudyViewFilterHelper(studyViewFilterContext), genomicDataFilter);
     }
 
     public List<GenomicDataCountItem> getMutationCountsByType(StudyViewFilterContext studyViewFilterContext, List<GenomicDataFilter> genomicDataFilters) {
-
         return mapper.getMutationCountsByType(createStudyViewFilterHelper(studyViewFilterContext), genomicDataFilters);
     }
 

diff --git a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java b/src/main/java/org/cbioportal/service/StudyViewColumnarService.java
@@ -5,6 +5,7 @@
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataCountItem;
 import org.cbioportal.model.ClinicalEventTypeCount;
+import org.cbioportal.model.GenericAssayDataCountItem;
 import org.cbioportal.model.GenomicDataCountItem;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.CopyNumberCountByGene;
@@ -14,6 +15,7 @@
 import org.cbioportal.service.exception.StudyNotFoundException;
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.GenericAssayDataBinFilter;
+import org.cbioportal.web.parameter.GenericAssayDataFilter;
 import org.cbioportal.web.parameter.GenomicDataBinFilter;
 import org.cbioportal.web.parameter.GenomicDataFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
@@ -46,6 +48,8 @@ public interface StudyViewColumnarService {
     SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter);
 
     List<GenomicDataCountItem> getCNACountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters);
+
+    List<GenericAssayDataCountItem> getGenericAssayDataCounts(StudyViewFilter studyViewFilter, List<GenericAssayDataFilter> genericAssayDataFilters);
 
     List<GenomicDataCountItem> getMutationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters);
 

diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -7,6 +7,7 @@
 import org.cbioportal.model.ClinicalDataCountItem;
 import org.cbioportal.model.ClinicalEventTypeCount;
 import org.cbioportal.model.CopyNumberCountByGene;
+import org.cbioportal.model.GenericAssayDataCountItem;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.PatientTreatmentReport;
 import org.cbioportal.model.GenomicDataCountItem;
@@ -21,6 +22,7 @@
 import org.cbioportal.web.parameter.ClinicalDataType;
 import org.cbioportal.web.parameter.CustomSampleIdentifier;
 import org.cbioportal.web.parameter.GenericAssayDataBinFilter;
+import org.cbioportal.web.parameter.GenericAssayDataFilter;
 import org.cbioportal.web.parameter.GenomicDataBinFilter;
 import org.cbioportal.web.parameter.GenomicDataFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
@@ -143,7 +145,12 @@ public List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter,
     public List<GenomicDataCountItem> getCNACountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
         return studyViewRepository.getCNACounts(createContext(studyViewFilter), genomicDataFilters);
     }
-
+
+    @Override
+    public List<GenericAssayDataCountItem> getGenericAssayDataCounts(StudyViewFilter studyViewFilter, List<GenericAssayDataFilter> genericAssayDataFilters) {
+        return studyViewRepository.getGenericAssayDataCounts(createContext(studyViewFilter), genericAssayDataFilters);
+    }
+
     @Override
     public List<GenomicDataCountItem> getMutationCountsByGeneSpecific(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters) {
         List<GenomicDataCountItem> genomicDataCountItemList = new ArrayList<>();

diff --git a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java b/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
@@ -20,6 +20,7 @@
 import org.cbioportal.model.CopyNumberCountByGene;
 import org.cbioportal.model.DensityPlotData;
 import org.cbioportal.model.GenericAssayDataBin;
+import org.cbioportal.model.GenericAssayDataCountItem;
 import org.cbioportal.model.GenomicDataBin;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.PatientTreatmentReport;
@@ -40,6 +41,8 @@
 import org.cbioportal.web.parameter.ClinicalDataFilter;
 import org.cbioportal.web.parameter.DataBinMethod;
 import org.cbioportal.web.parameter.GenericAssayDataBinCountFilter;
+import org.cbioportal.web.parameter.GenericAssayDataCountFilter;
+import org.cbioportal.web.parameter.GenericAssayDataFilter;
 import org.cbioportal.web.parameter.GenomicDataBinCountFilter;
 import org.cbioportal.web.parameter.GenomicDataCountFilter;
 import org.cbioportal.web.parameter.GenomicDataFilter;
@@ -399,6 +402,32 @@ public ResponseEntity<List<GenomicDataCountItem>> fetchGenomicDataCounts(
         return new ResponseEntity<>(result, HttpStatus.OK);
     }
 
+    @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
+    @PostMapping(value = "/column-store/generic-assay-data-counts/fetch", consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
+    @Operation(description = "Fetch generic assay data counts by study view filter")
+    @ApiResponse(responseCode = "200", description = "OK",
+        content = @Content(array = @ArraySchema(schema = @Schema(implementation = GenericAssayDataCountItem.class))))
+    public ResponseEntity<List<GenericAssayDataCountItem>> fetchGenericAssayDataCounts(
+        @Parameter(required = true, description = "Generic assay data count filter") @Valid @RequestBody(required = false) GenericAssayDataCountFilter genericAssayDataCountFilter,
+        @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 = "interceptedGenericAssayDataCountFilter") GenericAssayDataCountFilter interceptedGenericAssayDataCountFilter) {
+
+        List<GenericAssayDataFilter> gaFilters = interceptedGenericAssayDataCountFilter.getGenericAssayDataFilters();
+        StudyViewFilter studyViewFilter = interceptedGenericAssayDataCountFilter.getStudyViewFilter();
+        // when there is only one filter, it means study view is doing a single chart filter operation
+        // remove filter from studyViewFilter to return all data counts
+        // the reason we do this is to make sure after chart get filtered, user can still see unselected portion of the chart
+
+        if (gaFilters.size() == 1) {
+            studyViewFilterUtil.removeSelfFromGenericAssayFilter(gaFilters.getFirst().getStableId(), studyViewFilter);
+        }
+
+        return new ResponseEntity<>(studyViewColumnarService.getGenericAssayDataCounts(studyViewFilter, gaFilters), HttpStatus.OK);
+    }
+
     @PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
     @PostMapping(value = "/column-store/mutation-data-counts/fetch", consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
     @Operation(description = "Fetch mutation data counts by GenomicDataCountFilter")

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
@@ -442,6 +442,10 @@
                 <choose>
                     <when test="dataFilterValue.value == 'NA'">
                         empty(attribute_value)
+                        OR
+                        <include refid="normalizeAttributeValue">
+                            <property name="attribute_value" value="attribute_value"/>
+                        </include> = 'NA'
                     </when>
                     <otherwise>
                         (
@@ -541,13 +545,11 @@
             </foreach>
     </sql>
 
-    <sql id="selectAllNumericalGenericAssays">
-        SELECT sample_unique_id, value
+    <sql id="selectAllGenericAssays">
+        SELECT sample_unique_id, value, datatype
         FROM generic_assay_data_derived
         WHERE profile_type = #{genericAssayDataFilter.profileType}
             AND entity_stable_id = #{genericAssayDataFilter.stableId}
-            <!-- It needs to include all numerical data types. Currently it's only LIMIT-VALUE -->
-            AND datatype = 'LIMIT-VALUE'
     </sql>
 
     <!-- TODO: update the database scheme to include the data_type column -->
@@ -569,8 +571,9 @@
         <if test="userSelectsNA">
             SELECT DISTINCT sd.sample_unique_id
             FROM sample_derived sd
-                LEFT JOIN (<include refid="selectAllNumericalGenericAssays"/>) AS generic_numerical_query ON sd.sample_unique_id = generic_numerical_query.sample_unique_id
-            WHERE value IS null OR
+                LEFT JOIN (<include refid="selectAllGenericAssays"/>) AS generic_numerical_query ON sd.sample_unique_id = generic_numerical_query.sample_unique_id
+            WHERE datatype = 'LIMIT-VALUE'
+            AND value IS null OR
                 <include refid="normalizeAttributeValue">
                     <property name="attribute_value" value="value"/>
                 </include> = 'NA'
@@ -582,8 +585,10 @@
         <!-- if non-NA is selected, prepare non-NA samples -->
         <if test="userSelectsNumericalValue">
             SELECT DISTINCT sample_unique_id
-            FROM (<include refid="selectAllNumericalGenericAssays"/>) AS generic_numerical_query
+            FROM (<include refid="selectAllGenericAssays"/>) AS generic_numerical_query
             WHERE
+            datatype = 'LIMIT-VALUE'
+            AND
             <include refid="normalizeAttributeValue">
                 <property name="attribute_value" value="value"/>
             </include> != 'NA'
@@ -639,18 +644,29 @@
 
     <sql id="categoricalGenericAssayDataCountFilter">
         SELECT ${unique_id}
-        FROM ${table_name}
-        WHERE entity_stable_id = '${genericAssayDataFilter.stableId}' AND
-        profile_type='${genericAssayDataFilter.profileType}'
-        <foreach item="dataFilterValue" collection="genericAssayDataFilter.values" open=" AND ((" separator=") OR (" close="))">
-            <trim prefix="" prefixOverrides="AND">
-                AND (
-                <include refid="normalizeAttributeValue">
-                    <property name="attribute_value" value="value"/>
-                </include>
-                ) ILIKE '${dataFilterValue.value}'
-            </trim>
-        </foreach>
+        FROM sample_derived sd
+        LEFT JOIN (<include refid="selectAllGenericAssays"/>) AS generic_assay_query
+        ON sd.sample_unique_id = generic_assay_query.sample_unique_id 
+        <where>
+            datatype != 'LIMIT-VALUE' 
+            <foreach item="dataFilterValue" collection="genericAssayDataFilter.values" open=" AND ((" separator=") OR (" close="))">
+                <choose>
+                    <when test="dataFilterValue.value == 'NA'">
+                        value IS null OR
+                        <include refid="normalizeAttributeValue">
+                            <property name="attribute_value" value="value"/>
+                        </include> = 'NA'
+                    </when>
+                    <otherwise>
+                        (
+                        <include refid="normalizeAttributeValue">
+                            <property name="attribute_value" value="value"/>
+                        </include>
+                        ) ILIKE '${dataFilterValue.value}'
+                    </otherwise>
+                </choose>
+            </foreach>
+        </where>
     </sql>
 
     <sql id="applyMutationDataFilter">

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -282,6 +282,47 @@
             'NA' as value,
             cast(((SELECT * FROM (<include refid="getTotalSampleCount"/>)) - coalesce((SELECT cna_count FROM cna_sum LIMIT 1), 0)) as INTEGER) as count
     </select>
+
+    <select id="getGenericAssayDataCounts" resultMap="GenericAssayDataCountItemResultMap">
+        <bind name="profileType" value="genericAssayDataFilters[0].profileType"/> 
+        WITH generic_assay_query AS (
+            SELECT
+                entity_stable_id AS stableId,
+                value,
+                cast(count(*) AS INTEGER) AS count
+            FROM generic_assay_data_derived
+            <where>
+                <!-- Table creation in clickhouse.sql has ensured no NA values but extra caution is always appreciated -->
+                <include refid="normalizeAttributeValue">
+                    <property name="attribute_value" value="value"/>
+                </include> != 'NA' AND
+                profile_type = #{profileType} AND
+                <include refid="applyStudyViewFilter">
+                    <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
+                </include>
+                <foreach item="genericAssayDataFilter" collection="genericAssayDataFilters" open=" AND (" separator=" OR " close=")">
+                    entity_stable_id = #{genericAssayDataFilter.stableId}
+                </foreach> 
+            </where>
+            GROUP BY entity_stable_id, value
+        ),
+        generic_assay_data_sum AS (
+            SELECT
+                stableId,
+                sum(count) AS gad_count
+            FROM generic_assay_query
+            GROUP BY stableId
+        )
+
+        SELECT * FROM generic_assay_query
+        UNION ALL
+        <!-- The NA count is specially caculated using total sample count minus non-NA count, therefore 
+         these 2 coalesces are here in case the non-NA subquery returned empty results and we need to provide properties needed to construct the target object -->
+        SELECT
+        coalesce((SELECT stableId FROM generic_assay_data_sum LIMIT 1), #{genericAssayDataFilters[0].stableId}) as stableId,
+        'NA' as value,
+        cast(((SELECT * FROM (<include refid="getTotalSampleCount"/>)) - coalesce((SELECT gad_count FROM generic_assay_data_sum LIMIT 1), 0)) as INTEGER) as count 
+    </select>
 
     <!-- for /mutation-data-counts/fetch (returns GenomicDataCountItem objects) mutation counts pie chart part -->
     <select id="getMutationCounts">
@@ -346,6 +387,14 @@
             <result property="uniqueCount" column="uniqueCount"/>
         </collection>
     </resultMap>
+
+    <resultMap id="GenericAssayDataCountItemResultMap" type="org.cbioportal.model.GenericAssayDataCountItem">
+        <result property="stableId" column="stableId"/>
+        <collection property="counts" ofType="org.cbioportal.model.GenericAssayDataCount">
+            <result property="value" column="value"/>
+            <result property="count" column="count"/>
+        </collection>
+    </resultMap>
 
     <sql id="getPatientIdsFromSampleIdFilters">
         SELECT patient_unique_id