cBioPortal · alisman · Nov 6, 2024 · Oct 11, 2024 · Oct 14, 2024 · Oct 15, 2024
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -5,6 +5,7 @@
 import org.cbioportal.model.CaseListDataCount;
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataCount;
+import org.cbioportal.model.ClinicalDataCountItem;
 import org.cbioportal.model.ClinicalEventTypeCount;
 import org.cbioportal.model.CopyNumberCountByGene;
 import org.cbioportal.model.GenericAssayDataCountItem;
@@ -39,7 +40,7 @@ public interface StudyViewRepository {
     List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterContext studyViewFilterContext);
     List<CopyNumberCountByGene> getCnaGenes(StudyViewFilterContext studyViewFilterContext);
 
-    List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes);
+    List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes);
 
     List<GenomicDataCount> getMolecularProfileSampleCounts(StudyViewFilterContext studyViewFilterContext);
 

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -6,6 +6,7 @@
 import org.cbioportal.model.ClinicalAttribute;
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataCount;
+import org.cbioportal.model.ClinicalDataCountItem;
 import org.cbioportal.model.ClinicalEventTypeCount;
 import org.cbioportal.model.CopyNumberCountByGene;
 import org.cbioportal.model.GenePanelToGene;
@@ -40,7 +41,7 @@ public interface StudyViewMapper {
 
     List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterHelper studyViewFilterHelper, AlterationFilterHelper alterationFilterHelper);
 
-    List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds, List<String> filteredAttributeValues);
+    List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilterHelper studyViewFilterHelper, List<String> attributeIds, List<String> filteredAttributeValues);
 
     List<CaseListDataCount> getCaseListDataCountsPerStudy(@Param("studyViewFilterHelper") StudyViewFilterHelper studyViewFilterHelper);
 

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -4,6 +4,7 @@
 import org.cbioportal.model.CaseListDataCount;
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataCount;
+import org.cbioportal.model.ClinicalDataCountItem;
 import org.cbioportal.model.ClinicalEventTypeCount;
 import org.cbioportal.model.GenePanelToGene;
 import org.cbioportal.model.GenericAssayDataCountItem;
@@ -79,7 +80,7 @@ public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilterCont
     }
 
     @Override
-    public List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes) {
+    public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes) {
         return mapper.getClinicalDataCounts(createStudyViewFilterHelper(studyViewFilterContext),
             filteredAttributes, FILTERED_CLINICAL_ATTR_VALUES);
     }

diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -153,17 +153,7 @@ public Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap() {
     )
     @Override
     public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
-        StudyViewFilterContext studyViewFilterContext = createContext(studyViewFilter);
-        List<ClinicalDataCount> dataCounts = studyViewRepository.getClinicalDataCounts(studyViewFilterContext, filteredAttributes);
-        List<ClinicalDataCountItem> clinicalDataCountItems = generateDataCountItemsFromDataCounts(dataCounts);
-
-        return calculateMissingNaCountsForClinicalDataCountItems(
-            clinicalDataCountItems,
-            filteredAttributes.stream().distinct().toList(),
-            this.getClinicalAttributeDatatypeMap(),
-            studyViewRepository.getFilteredSamplesCount(studyViewFilterContext),
-            studyViewRepository.getFilteredPatientCount(studyViewFilterContext)
-        );
+       return studyViewRepository.getClinicalDataCounts(createContext(studyViewFilter), filteredAttributes); 
     }
 
     @Cacheable(
@@ -311,83 +301,6 @@ private List<ClinicalDataCount> normalizeDataCounts(List<ClinicalDataCount> data
         return new ArrayList<>(normalizedDataCounts);
     }
 
-    public static List<ClinicalDataCountItem> calculateMissingNaCountsForClinicalDataCountItems(
-        List<ClinicalDataCountItem> clinicalDataCountItems,
-        List<String> filteredAttributes,
-        Map<String, ClinicalDataType> clinicalAttributeDatatypeMap,
-        int filteredSamplesCount,
-        int filteredPatientsCount
-    ) {
-        // Postprocess clinical data count items to adjust NA counts
-        List<ClinicalDataCountItem> combinedClinicalDataCountItems = new ArrayList<>();
-
-        Map<String, ClinicalDataCountItem> clinicalDataCountItemMap = clinicalDataCountItems
-            .stream()
-            .collect(Collectors.toMap(
-                ClinicalDataCountItem::getAttributeId,
-                item -> item
-            ));
-
-        // go over all filtered attributes, not just attributes found in clinicalDataCountItems
-        for (String attributeId: filteredAttributes) {
-            ClinicalDataCountItem clinicalDataCountItem = clinicalDataCountItemMap.get(attributeId);
-            boolean isItemMissing = false;
-
-            if (clinicalDataCountItem == null) {
-                isItemMissing = true;
-                clinicalDataCountItem = new ClinicalDataCountItem();
-                clinicalDataCountItem.setAttributeId(attributeId);
-                clinicalDataCountItem.setCounts(new ArrayList<>());
-            }
-
-            Integer totalClinicalDataCount = clinicalDataCountItem
-                .getCounts()
-                .stream()
-                .map(ClinicalDataCount::getCount)
-                .reduce(0, Integer::sum);
-            // depending on clinical data type we either use filtered sample count or filtered patient count
-            int filteredCount = clinicalAttributeDatatypeMap.get(clinicalDataCountItem.getAttributeId()) == ClinicalDataType.SAMPLE ?
-                filteredSamplesCount: filteredPatientsCount;
-            int casesWithoutClinicalData = filteredCount - totalClinicalDataCount;
-
-            if (casesWithoutClinicalData > 0) {
-                // some of these attributes may be completely missing in clinicalDataCountItem
-                // in case the only attribute value is NA.
-                // we need to manually add those missing items to make sure we have NA counts.
-                if (isItemMissing) {
-                    combinedClinicalDataCountItems.add(clinicalDataCountItem);
-                }
-
-                // find "NA" or else create a new one
-                Optional<ClinicalDataCount> naClinicalDataCountOptional = clinicalDataCountItem
-                    .getCounts()
-                    .stream()
-                    .filter(c -> c.getValue().equals("NA"))
-                    .findFirst();
-
-                ClinicalDataCount naClinicalDataCount = naClinicalDataCountOptional
-                    .orElseGet(() -> {
-                        // this should only happen when there are multiple studies
-                        ClinicalDataCount count = new ClinicalDataCount();
-                        count.setAttributeId(attributeId);
-                        count.setValue("NA");
-                        count.setCount(0);
-                        return count;
-                    });
-
-                // if not present we need to add naClinicalDataCount to the existing counts
-                if (naClinicalDataCountOptional.isEmpty()) {
-                    clinicalDataCountItem.getCounts().add(naClinicalDataCount);
-                }
-
-                naClinicalDataCount.setCount(naClinicalDataCount.getCount() + casesWithoutClinicalData);
-            }
-        }
-
-        combinedClinicalDataCountItems.addAll(clinicalDataCountItems);
-        return combinedClinicalDataCountItems;
-    }
-
     public static List<CaseListDataCount> mergeCaseListCounts(List<CaseListDataCount> counts) {
         Map<String, List<CaseListDataCount>> countsPerListType = counts.stream()
             .collect((Collectors.groupingBy(CaseListDataCount::getValue)));

diff --git a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java b/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
@@ -208,12 +208,10 @@ public ResponseEntity<List<ClinicalDataCountItem>> fetchClinicalDataCounts(
         StudyViewFilter studyViewFilter = interceptedClinicalDataCountFilter.getStudyViewFilter();
 
         if (attributes.size() == 1) {
-            NewStudyViewFilterUtil.removeSelfFromFilter(attributes.get(0).getAttributeId(), studyViewFilter);
+            NewStudyViewFilterUtil.removeClinicalDataFilter(attributes.getFirst().getAttributeId(), studyViewFilter.getClinicalDataFilters());
        }
-       // boolean singleStudyUnfiltered = studyViewFilterUtil.isSingleStudyUnfiltered(studyViewFilter);
         List<ClinicalDataCountItem> result = studyViewColumnarService.getClinicalDataCounts(studyViewFilter, 
             attributes.stream().map(ClinicalDataFilter::getAttributeId).collect(Collectors.toList()));
-            //studyIds, sampleIds, attributes.stream().map(a -> a.getAttributeId()).collect(Collectors.toList())); 
         return new ResponseEntity<>(result, HttpStatus.OK);
 
     }
@@ -576,7 +574,7 @@ public ResponseEntity<List<ClinicalDataCountItem>> fetchCustomDataCounts(
         List<ClinicalDataFilter> attributes = interceptedClinicalDataCountFilter.getAttributes();
         StudyViewFilter studyViewFilter = interceptedClinicalDataCountFilter.getStudyViewFilter();
         if (attributes.size() == 1) {
-            NewStudyViewFilterUtil.removeSelfCustomDataFromFilter(attributes.get(0).getAttributeId(), studyViewFilter);
+            NewStudyViewFilterUtil.removeClinicalDataFilter(attributes.getFirst().getAttributeId(), studyViewFilter.getCustomDataFilters());
         }
 
         List <SampleIdentifier> filteredSampleIdentifiers = studyViewColumnarService.getFilteredSamples(studyViewFilter).stream().map(sample -> studyViewFilterUtil.buildSampleIdentifier(sample.getCancerStudyIdentifier(), sample.getStableId())).toList();

diff --git a/src/main/java/org/cbioportal/web/columnar/util/NewClinicalDataBinUtil.java b/src/main/java/org/cbioportal/web/columnar/util/NewClinicalDataBinUtil.java
@@ -25,7 +25,7 @@ public static StudyViewFilter removeSelfFromFilter(ClinicalDataBinCountFilter da
         StudyViewFilter studyViewFilter = dataBinCountFilter.getStudyViewFilter();
 
         if (attributes.size() == 1) {
-            NewStudyViewFilterUtil.removeSelfFromFilter(attributes.get(0).getAttributeId(), studyViewFilter);
+            NewStudyViewFilterUtil.removeClinicalDataFilter(attributes.getFirst().getAttributeId(), studyViewFilter.getClinicalDataFilters());
         }
 
         return studyViewFilter;
@@ -36,7 +36,7 @@ public static StudyViewFilter removeSelfCustomDataFromFilter(ClinicalDataBinCoun
         StudyViewFilter studyViewFilter = dataBinCountFilter.getStudyViewFilter();
 
         if (attributes.size() == 1) {
-            NewStudyViewFilterUtil.removeSelfCustomDataFromFilter(attributes.get(0).getAttributeId(), studyViewFilter);
+            NewStudyViewFilterUtil.removeClinicalDataFilter(attributes.getFirst().getAttributeId(), studyViewFilter.getCustomDataFilters());
         }
 
         return studyViewFilter;

diff --git a/src/main/java/org/cbioportal/web/columnar/util/NewStudyViewFilterUtil.java b/src/main/java/org/cbioportal/web/columnar/util/NewStudyViewFilterUtil.java
@@ -1,19 +1,15 @@
 package org.cbioportal.web.columnar.util;
 
 
-import org.cbioportal.web.parameter.StudyViewFilter;
+import org.cbioportal.web.parameter.ClinicalDataFilter;
 
-public class NewStudyViewFilterUtil {
+import java.util.List;
 
-    public static void removeSelfFromFilter(String attributeId, StudyViewFilter studyViewFilter) {
-        if (studyViewFilter!= null && studyViewFilter.getClinicalDataFilters() != null) {
-            studyViewFilter.getClinicalDataFilters().removeIf(f -> f.getAttributeId().equals(attributeId));
-        }
-    }
+public class NewStudyViewFilterUtil {
 
-    public static void removeSelfCustomDataFromFilter(String attributeId, StudyViewFilter studyViewFilter) {
-        if (studyViewFilter != null && studyViewFilter.getCustomDataFilters() != null) {
-            studyViewFilter.getCustomDataFilters().removeIf(f -> f.getAttributeId().equals(attributeId));
+    public static void removeClinicalDataFilter(String attributeId, List<ClinicalDataFilter> dataFilterList ) {
+        if (dataFilterList != null) {
+            dataFilterList.removeIf(f -> f.getAttributeId().equals(attributeId));
         }
     }
 }
diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -136,10 +136,14 @@
     </select>
 
     <!-- for /clinical-data-counts/fetch (returns ClinicalData) which will then be converted to clinicalDataCountItems -->
-    <select id="getClinicalDataCounts" resultType="org.cbioportal.model.ClinicalDataCount">
-        <include refid="getClinicalDataCountsQuerySample" />
+    <select id="getClinicalDataCounts" resultMap="ClinicalDataCountItemResultMap">
+        <include refid="getClinicalDataCountsQuery">
+            <property name="type" value="sample"/>
+        </include>
         UNION ALL
-        <include refid="getClinicalDataCountsQueryPatient" />
+        <include refid="getClinicalDataCountsQuery">
+            <property name="type" value="patient"/>
+        </include>
     </select>
 
     <!-- for /molecular-profile-sample-counts/fetch (returns GenomicDataCount) which will then be converted to clinicalDataCountItems -->
@@ -179,63 +183,63 @@
         GROUP BY s.cancer_study_identifier, sl.stable_id, sl.name
     </select>
 
-
-    <sql id="getClinicalDataCountsQuerySample">
+    <sql id="getClinicalDataCountsQuery">
+        (
+        WITH clinical_data_query AS (
         SELECT
-        attribute_name as attributeId,
-        <include refid="normalizeAttributeValue">
-            <property name="attribute_value" value="attribute_value"/>
-        </include> as value,
-        count(value) as count
+        attribute_name AS attributeId,
+        upper(attribute_value) AS value,
+        cast(count(*) AS INTEGER) as count
         FROM clinical_data_derived
         <where>
-            type='sample' AND
-            <include refid="applyStudyViewFilter">
-                <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
+            type='${type}'
+            AND <!-- Table creation in clickhouse.sql has ensured no NA values but extra caution is always appreciated -->
+            <include refid="normalizeAttributeValue">
+                <property name="attribute_value" value="value"/>
             </include>
-            <if test="filteredAttributeValues != null and !filteredAttributeValues.isEmpty()">
-                AND UPPER(value) NOT IN
-                <foreach item="filteredAttributeValue" collection="filteredAttributeValues" open="(" separator="," close=")">
-                    #{filteredAttributeValue}
-                </foreach>
-            </if>
+            != 'NA'
+            AND
+            <choose>
+                <when test="'${type}' == 'sample'">
+                    <include refid="applyStudyViewFilter">
+                        <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
+                    </include>
+                </when>
+                <otherwise>
+                    <include refid="applyStudyViewFilter">
+                        <property name="filter_type" value="'PATIENT_ID_ONLY'"/>
+                    </include>
+                </otherwise>
+            </choose>
             AND attribute_name IN
             <foreach item="attributeId" collection="attributeIds" open="(" separator="," close=")">
                 #{attributeId}
             </foreach>
         </where>
-        GROUP BY attribute_name,
-        value
-    </sql>
-
-    <sql id="getClinicalDataCountsQueryPatient">
-        SELECT
-        attribute_name as attributeId,
-        <include refid="normalizeAttributeValue">
-            <property name="attribute_value" value="attribute_value"/>
-        </include> as value,
-        count(value) as count
-        FROM clinical_data_derived
+        GROUP BY attribute_name, value ),
+        clinical_data_sum AS (SELECT attributeId, sum(count) AS sum FROM clinical_data_query GROUP BY attributeId)
+
+        SELECT * FROM clinical_data_query
+        UNION ALL
+        SELECT attributeId,
+            'NA' AS value,
+            ((
+                <choose>
+                    <when test="'${type}' == 'sample'">
+                        <include refid="getTotalSampleCount"/>
+                    </when>
+                    <otherwise>
+                        <include refid="getTotalPatientCount"/>    
+                    </otherwise>
+                </choose>
+        ) - clinical_data_sum.sum) AS count
+        FROM clinical_data_sum
         <where>
-            type='patient' AND
-            <include refid="applyStudyViewFilter">
-                <property name="filter_type" value="'PATIENT_ID_ONLY'"/>
-            </include>
-            <if test="filteredAttributeValues != null and !filteredAttributeValues.isEmpty()">
-                AND UPPER(value) NOT IN
-                <foreach item="filteredAttributeValue" collection="filteredAttributeValues" open="(" separator="," close=")">
-                    #{filteredAttributeValue}
-                </foreach>
-            </if>
-            AND attribute_name IN
-            <foreach item="attributeId" collection="attributeIds" open="(" separator="," close=")">
-                #{attributeId}
-            </foreach>
+            count > 0
         </where>
-        GROUP BY attribute_name,
-        value
+        )
     </sql>
-
+    
     <sql id="getTotalSampleCount">
         SELECT count(distinct sample_unique_id) as count
         FROM sample_derived
@@ -409,6 +413,15 @@
             <result property="count" column="count"/>
         </collection>
     </resultMap>
+
+    <resultMap id="ClinicalDataCountItemResultMap" type="org.cbioportal.model.ClinicalDataCountItem">
+        <result property="attributeId" column="attributeId"/>
+        <collection property="counts" ofType="org.cbioportal.model.ClinicalDataCount">
+            <result property="attributeId" column="attributeId"/>
+            <result property="value" column="value"/>
+            <result property="count" column="count"/>
+        </collection>
+    </resultMap>
 
     <sql id="getPatientIdsFromSampleIdFilters">
         SELECT patient_unique_id