use the exact same queries which have been used for the clinical data…

… counts endpoint
cBioPortal · Jun 27, 2024 · f7905ff · f7905ff
1 parent b63c104
commit f7905ff
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Showing 9 changed files with 41 additions and 54 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -21,9 +21,9 @@ public interface StudyViewRepository {
 
     List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds);
 
-    List<ClinicalDataCount>getSampleClinicalDataCountsForBinning(StudyViewFilter studyViewFilter, List<String> attributeIds);
+    List<ClinicalDataCount> getSampleClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> attributeIds);
 
-    List<ClinicalDataCount>getPatientClinicalDataCountsForBinning(StudyViewFilter studyViewFilter, List<String> attributeIds);
+    List<ClinicalDataCount> getPatientClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> attributeIds);
 
     List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter);
 

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -49,10 +49,6 @@ List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, C
 
     List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds);
 
-    List<ClinicalDataCount> getSampleClinicalDataCountsForBinning(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds);
-
-    List<ClinicalDataCount> getPatientClinicalDataCountsForBinning(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds);
-
     @MapKey("hugoGeneSymbol")
     Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
 

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -101,14 +101,26 @@ public List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter,
         return mapper.getSampleClinicalDataFromStudyViewFilter(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), attributeIds);
     }
 
-    public List<ClinicalDataCount> getSampleClinicalDataCountsForBinning(StudyViewFilter studyViewFilter, List<String> attributeIds) {
+    public List<ClinicalDataCount> getSampleClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> attributeIds) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
-        return mapper.getSampleClinicalDataCountsForBinning(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), attributeIds);
+        return mapper.getSampleClinicalDataCounts(
+            studyViewFilter,
+            categorizedClinicalDataCountFilter,
+            shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
+            attributeIds,
+            FILTERED_CLINICAL_ATTR_VALUES
+        );
     }
 
-    public List<ClinicalDataCount> getPatientClinicalDataCountsForBinning(StudyViewFilter studyViewFilter, List<String> attributeIds) {
+    public List<ClinicalDataCount> getPatientClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> attributeIds) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
-        return mapper.getPatientClinicalDataCountsForBinning(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), attributeIds);
+        return mapper.getPatientClinicalDataCounts(
+            studyViewFilter,
+            categorizedClinicalDataCountFilter,
+            shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
+            attributeIds,
+            FILTERED_CLINICAL_ATTR_VALUES
+        );
     }
 
     @Override

diff --git a/src/main/java/org/cbioportal/service/StudyViewColumnarService.java b/src/main/java/org/cbioportal/service/StudyViewColumnarService.java
@@ -28,9 +28,9 @@ public interface StudyViewColumnarService {
 
     List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds);
 
-    List<ClinicalDataCount> getSampleClinicalDataCountsForBinning(StudyViewFilter studyViewFilter, List<String> attributeIds);
+    List<ClinicalDataCount> getSampleClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> attributeIds);
 
-    List<ClinicalDataCount> getPatientClinicalDataCountsForBinning(StudyViewFilter studyViewFilter, List<String> attributeIds);
+    List<ClinicalDataCount> getPatientClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> attributeIds);
 
     List<GenomicDataCount> getGenomicDataCounts(StudyViewFilter studyViewFilter);
 

diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -87,13 +87,13 @@ public List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter,
     }
 
     @Override
-    public List<ClinicalDataCount> getSampleClinicalDataCountsForBinning(StudyViewFilter studyViewFilter, List<String> attributeIds) {
-        return studyViewRepository.getSampleClinicalDataCountsForBinning(studyViewFilter, attributeIds);
+    public List<ClinicalDataCount> getSampleClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> attributeIds) {
+        return studyViewRepository.getSampleClinicalDataCounts(studyViewFilter, attributeIds);
     }
 
     @Override
-    public List<ClinicalDataCount> getPatientClinicalDataCountsForBinning(StudyViewFilter studyViewFilter, List<String> attributeIds) {
-        return studyViewRepository.getPatientClinicalDataCountsForBinning(studyViewFilter, attributeIds);
+    public List<ClinicalDataCount> getPatientClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> attributeIds) {
+        return studyViewRepository.getPatientClinicalDataCounts(studyViewFilter, attributeIds);
     }
 
 }
diff --git a/src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java b/src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java
@@ -66,10 +66,10 @@ public List<ClinicalDataBin> fetchClinicalDataBinCounts(
         // we use the filtered data to calculate the counts for each bin, we do not regenerate bins for the filtered data 
 
         // TODO investigate if we can directly use studyViewColumnarService.getClinicalDataCounts instead of adding new SQL
-        List<ClinicalDataCount> unfilteredClinicalDataCountsForSamples = studyViewColumnarService.getSampleClinicalDataCountsForBinning(partialFilter, attributeIds);
-        List<ClinicalDataCount> filteredClinicalDataCountsForSamples = studyViewColumnarService.getSampleClinicalDataCountsForBinning(studyViewFilter, attributeIds);
-        List<ClinicalDataCount> unfilteredClinicalDataCountsForPatients = studyViewColumnarService.getPatientClinicalDataCountsForBinning(partialFilter, attributeIds);
-        List<ClinicalDataCount> filteredClinicalDataCountsForPatients = studyViewColumnarService.getPatientClinicalDataCountsForBinning(studyViewFilter, attributeIds);
+        List<ClinicalDataCount> unfilteredClinicalDataCountsForSamples = studyViewColumnarService.getSampleClinicalDataCounts(partialFilter, attributeIds);
+        List<ClinicalDataCount> filteredClinicalDataCountsForSamples = studyViewColumnarService.getSampleClinicalDataCounts(studyViewFilter, attributeIds);
+        List<ClinicalDataCount> unfilteredClinicalDataCountsForPatients = studyViewColumnarService.getPatientClinicalDataCounts(partialFilter, attributeIds);
+        List<ClinicalDataCount> filteredClinicalDataCountsForPatients = studyViewColumnarService.getPatientClinicalDataCounts(studyViewFilter, attributeIds);
 
         List<ClinicalData> unfilteredClinicalDataForSamples = convertCountsToData(unfilteredClinicalDataCountsForSamples);
         List<ClinicalData> filteredClinicalDataForSamples = convertCountsToData(filteredClinicalDataCountsForSamples);

diff --git a/...khouse/StudyViewClinicalDataBinMapper.xml → ...lickhouse/StudyViewClinicalDataMapper.xml b/...khouse/StudyViewClinicalDataBinMapper.xml → ...lickhouse/StudyViewClinicalDataMapper.xml
@@ -35,34 +35,6 @@
             </foreach>
         </if>
     </sql>
-
-    <select id="getPatientClinicalDataCountsForBinning">
-        SELECT
-            attribute_name as attributeId,
-            <include refid="normalizeAttributeValueNA">
-                <property name="attribute_value" value="attribute_value"/>
-                <property name="as_value" value="value"/>
-            </include>,
-            count(value) as count
-        FROM clinical_data_derived
-        <include refid="patientClinicalDataFromStudyViewFilter" />
-        AND type = 'patient'
-        GROUP BY attribute_name, value
-    </select>
-
-    <select id="getSampleClinicalDataCountsForBinning">
-        SELECT
-            attribute_name as attributeId,
-            <include refid="normalizeAttributeValueNA">
-                <property name="attribute_value" value="attribute_value"/>
-                <property name="as_value" value="value"/>
-            </include>,
-            count(value) as count
-        FROM clinical_data_derived
-        <include refid="sampleClinicalDataFromStudyViewFilter" />
-        AND type = 'sample'
-        GROUP BY attribute_name, value
-    </select>
 
     <select id="getSampleClinicalDataFromStudyViewFilter" resultType="org.cbioportal.model.ClinicalData">
         SELECT

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -76,11 +76,18 @@
 
     <!-- for /clinical-data-counts/fetch (returns ClinicalData) which will then be converted to clinicalDataCountItems -->
     <select id="getClinicalDataCounts" resultType="org.cbioportal.model.ClinicalDataCount">
-        <include refid="getCategoricalClinicalDataCountsQuerySample" />
+        <include refid="getClinicalDataCountsQuerySample" />
         UNION ALL
-        <include refid="getCategoricalClinicalDataCountsQueryPatient" />
+        <include refid="getClinicalDataCountsQueryPatient" />
     </select>
 
+    <select id="getPatientClinicalDataCounts" resultType="org.cbioportal.model.ClinicalDataCount">
+        <include refid="getClinicalDataCountsQueryPatient" />
+    </select>
+
+    <select id="getSampleClinicalDataCounts" resultType="org.cbioportal.model.ClinicalDataCount">
+        <include refid="getClinicalDataCountsQuerySample" />
+    </select>
 
     <!-- for /molecular-profile-sample-counts/fetch (returns GenomicDataCount) which will then be converted to clinicalDataCountItems -->
     <select id="getGenomicDataCounts" resultType="org.cbioportal.model.GenomicDataCount">
@@ -115,7 +122,7 @@
     </select>
 
 
-    <sql id="getCategoricalClinicalDataCountsQuerySample">
+    <sql id="getClinicalDataCountsQuerySample">
         SELECT
         attribute_name as attributeId,
         <include refid="normalizeAttributeValueNA">
@@ -148,7 +155,7 @@
         value
     </sql>
 
-    <sql id="getCategoricalClinicalDataCountsQueryPatient">
+    <sql id="getClinicalDataCountsQueryPatient">
         SELECT
         attribute_name as attributeId,
         <include refid="normalizeAttributeValueNA">

diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/config/MyBatisConfig.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/config/MyBatisConfig.java
@@ -35,9 +35,9 @@ public SqlSessionFactoryBean sqlColumnarSessionFactory(ResourceLoader resourceLo
         var studyViewMapperResource = resourceLoader.getResource("classpath:org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml") ;
         var studyViewFilterMapperResource = resourceLoader.getResource("classpath:org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml");
         var alterationFilterMapperResource = resourceLoader.getResource("classpath:org/cbioportal/persistence/mybatisclickhouse/StudyViewAlterationFilterMapper.xml");
-        var clinicalDataBinMapperResource = resourceLoader.getResource("classpath:org/cbioportal/persistence/mybatisclickhouse/StudyViewAlterationFilterMapper.xml");
+        var clinicalDataMapperResource = resourceLoader.getResource("classpath:org/cbioportal/persistence/mybatisclickhouse/StudyViewClinicalDataMapper.xml");
         sessionFactory.setMapperLocations(
-            studyViewMapperResource,studyViewFilterMapperResource, alterationFilterMapperResource, clinicalDataBinMapperResource
+            studyViewMapperResource,studyViewFilterMapperResource, alterationFilterMapperResource, clinicalDataMapperResource
         );
         return sessionFactory;
     }