Fix case list filtering/counting

cBioPortal · Jun 20, 2024 · adec9e2 · adec9e2
1 parent 2b5547a
commit adec9e2
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Showing 6 changed files with 24 additions and 16 deletions.
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -1,15 +1,18 @@
 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.ClinicalData;
 import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.Sample;
+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 {

diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -1,12 +1,14 @@
 package org.cbioportal.persistence.mybatisclickhouse;
 import org.cbioportal.model.AlterationCountByGene;
+import org.cbioportal.model.CaseListDataCount;
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataCount;
 import org.cbioportal.model.GenomicDataCount;
 import org.cbioportal.model.Sample;
 import org.cbioportal.persistence.StudyViewRepository;
 import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
 import org.cbioportal.persistence.enums.ClinicalAttributeDataType;
+import org.cbioportal.persistence.helper.AlterationFilterHelper;
 import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
 import org.cbioportal.web.parameter.StudyViewFilter;
 import org.springframework.beans.factory.annotation.Autowired;

diff --git a/src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java b/src/main/java/org/cbioportal/web/columnar/ClinicalDataBinner.java
@@ -6,6 +6,7 @@
 import org.cbioportal.web.parameter.*;
 import org.cbioportal.web.util.DataBinner;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Component;
 
 import java.util.*;
@@ -26,6 +27,9 @@ public ClinicalDataBinner(
         this.dataBinner = dataBinner;
     }
 
+    @Cacheable(
+        cacheResolver = "staticRepositoryCacheOneResolver"
+    )
     public List<ClinicalDataBin> fetchClinicalDataBinCounts(
         DataBinMethod dataBinMethod,
         ClinicalDataBinCountFilter dataBinCountFilter,

diff --git a/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java b/src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
@@ -8,6 +8,7 @@
 import jakarta.validation.Valid;
 import org.cbioportal.model.AlterationCountByGene;
 import org.cbioportal.model.AlterationFilter;
+import org.cbioportal.model.CaseListDataCount;
 import org.cbioportal.model.ClinicalData;
 import org.cbioportal.model.ClinicalDataBin;
 import org.cbioportal.model.ClinicalDataCountItem;

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
@@ -16,21 +16,20 @@
             <!-- filter for samples which belong to the sample lists (aka case lists) selected by the user and appearing in the studyViewFilter.caseLists collection -->
             <if test="studyViewFilter.caseLists != null and !studyViewFilter.caseLists.isEmpty()">
                 INTERSECT
-                SELECT sample_unique_id
-                FROM sample_list_list sll
-                    LEFT JOIN sample_view sv ON sll.sample_id=sv.internal_id
-                    LEFT JOIN sample_list sl on sll.list_id=sl.list_id
-                <!-- a sample is in a sample list if the sampleListId is part of the sample's list stable id (stable_id) -->
-                <where>
-                    <foreach item="sampleLists" collection="studyViewFilter.caseLists" separator="INTERSECT">
-                        <foreach item="sampleListId" collection="sampleLists" open="(" separator="OR" close=")">
-                            stable_id LIKE '%_${sampleListId}'
+                SELECT * FROM (
+                    <foreach item="listGroup" collection="studyViewFilter.caseLists" separator="INTERSECT">
+                        SELECT sample_unique_id
+                        FROM sample_list_list sll
+                        LEFT JOIN sample_mv s ON sll.sample_id=s.internal_id
+                        LEFT JOIN sample_list sl on sll.list_id=sl.list_id
+                        WHERE
+                        <foreach item="list" collection="listGroup" separator="OR">
+                            sl.stable_id LIKE '%_${list}'
                         </foreach>
                     </foreach>
-                </where>
+                )
             </if>
-
-
+
             <if test="studyViewFilter.genomicProfiles != null and !studyViewFilter.genomicProfiles.isEmpty()">
                 INTERSECT
                 SELECT * FROM (
@@ -50,7 +49,6 @@
                             gp.stable_id LIKE '%_${genomicProfileId}'
                         </foreach>
                     </where>
-
                 </foreach>
                 )
 

diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -129,12 +129,12 @@
             REPLACE(stable_id, CONCAT(cancer_study_identifier, '_'), '') AS value,
             count(sample_id) AS count
         FROM sample_list_list sll
-             LEFT JOIN sample_view sv ON sll.sample_id=sv.internal_id
-             LEFT JOIN sample_list sl on sll.list_id=sl.list_id
+            LEFT JOIN sample_mv s ON sll.sample_id=s.internal_id
+            LEFT JOIN sample_list sl on sll.list_id=sl.list_id
         <where>
             sample_unique_id IN ( <include refid="sampleUniqueIdsFromStudyViewFilter"/>)
         </where>
-        GROUP BY cancer_study_identifier, stable_id, name;
+        GROUP BY s.cancer_study_identifier, sl.stable_id, sl.name;
     </select>
 
     <sql id="getCategoricalClinicalDataCountsQuery">