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cBioPortal · Feb 27, 2025 · 62abff3 · 62abff3
1 parent 3ef5db7
commit 62abff3
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Showing 6 changed files with 120 additions and 61 deletions.
diff --git a/src/main/java/org/cbioportal/domain/clinical_data/repository/ClinicalDataRepository.java b/src/main/java/org/cbioportal/domain/clinical_data/repository/ClinicalDataRepository.java
@@ -3,6 +3,7 @@
 import org.cbioportal.legacy.model.ClinicalData;
 import org.cbioportal.legacy.model.ClinicalDataCountItem;
 import org.cbioportal.domain.studyview.StudyViewFilterContext;
+import org.cbioportal.shared.enums.ProjectionType;
 
 import java.util.List;
 
@@ -18,11 +19,9 @@ public interface ClinicalDataRepository {
      * @param filteredAttributes A list of attributes to filter the clinical data.
      * @return A list of {@link ClinicalData} representing patient clinical data.
      */
-    List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes);
+    List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes);
 
-    List<ClinicalData> getPatientClinicalDataSummary(List<String> studyIds, List<String> sampleIds, List<String> filteredAttributes);
-
-    List<ClinicalData> getPatientClinicalDataDetailed(List<String> studyIds, List<String> sampleIds, List<String> filteredAttributes);
+    List<ClinicalData> getPatientClinicalData(List<String> studyIds, List<String> sampleIds, List<String> filteredAttributes, ProjectionType projectionType);
 
     /**
      * Retrieves clinical data for samples based on the given study view filter context and filtered attributes.
@@ -31,11 +30,9 @@ public interface ClinicalDataRepository {
      * @param filteredAttributes A list of attributes to filter the clinical data.
      * @return A list of {@link ClinicalData} representing sample clinical data.
      */
-    List<ClinicalData> getSampleClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes);
+    List<ClinicalData> getSampleClinicalDataFromStudyViewFilter(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes);
 
-    List<ClinicalData> getSampleClinicalDataSummary(List<String> studyIds, List<String> sampleIds, List<String> filteredAttributes);
-
-    List<ClinicalData> getSampleClinicalDataDetailed(List<String> studyIds, List<String> sampleIds, List<String> filteredAttributes);
+    List<ClinicalData> getSampleClinicalData(List<String> studyIds, List<String> sampleIds, List<String> filteredAttributes, ProjectionType projectionType);
 
     /**
      * Retrieves counts of clinical data records based on the given study view filter context and filtered attributes.

diff --git a/src/main/java/org/cbioportal/domain/clinical_data/usecase/GetPatientClinicalDataUseCase.java b/src/main/java/org/cbioportal/domain/clinical_data/usecase/GetPatientClinicalDataUseCase.java
@@ -40,7 +40,7 @@ public GetPatientClinicalDataUseCase(ClinicalDataRepository clinicalDataReposito
      * @return a list of {@link ClinicalData} representing the patient's clinical data
      */
     public List<ClinicalData> execute(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes) {
-        return clinicalDataRepository.getPatientClinicalData(studyViewFilterContext, filteredAttributes);
+        return clinicalDataRepository.getPatientClinicalDataFromStudyViewFilter(studyViewFilterContext, filteredAttributes);
     }
 
     public List<ClinicalData> execute(ClinicalDataMultiStudyFilter clinicalDataMultiStudyFilter, List<String> attributeIds, ProjectionType projectionType) {
@@ -51,20 +51,7 @@ public List<ClinicalData> execute(ClinicalDataMultiStudyFilter clinicalDataMulti
             patientIds.add(identifier.getEntityId());
         }
 
-        // DETAILED level
-        if (projectionType == ProjectionType.DETAILED) {
-            return clinicalDataRepository.getPatientClinicalDataDetailed(studyIds, patientIds, attributeIds);
-        }
-
-        // ID or SUMMARY level
-        List<ClinicalData> clinicalDataList = clinicalDataRepository.getPatientClinicalDataSummary(studyIds, patientIds, attributeIds);
-        // ID level doesn't have attrValue
-        if (projectionType == ProjectionType.ID) {
-            for (ClinicalData clinicalData : clinicalDataList) {
-                clinicalData.setAttrValue(null);
-            }
-        }
-        return clinicalDataList;
+        return clinicalDataRepository.getPatientClinicalData(studyIds, patientIds, attributeIds, projectionType);
     }
 }
 
diff --git a/src/main/java/org/cbioportal/domain/clinical_data/usecase/GetSampleClinicalDataUseCase.java b/src/main/java/org/cbioportal/domain/clinical_data/usecase/GetSampleClinicalDataUseCase.java
@@ -40,7 +40,7 @@ public GetSampleClinicalDataUseCase(ClinicalDataRepository clinicalDataRepositor
      * @return a list of {@link ClinicalData} representing the sample's clinical data
      */
     public List<ClinicalData> execute(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes) {
-        return clinicalDataRepository.getSampleClinicalData(studyViewFilterContext, filteredAttributes);
+        return clinicalDataRepository.getSampleClinicalDataFromStudyViewFilter(studyViewFilterContext, filteredAttributes);
     }
 
     public List<ClinicalData> execute(ClinicalDataMultiStudyFilter clinicalDataMultiStudyFilter, List<String> attributeIds, ProjectionType projectionType) {
@@ -51,20 +51,7 @@ public List<ClinicalData> execute(ClinicalDataMultiStudyFilter clinicalDataMulti
             sampleIds.add(identifier.getEntityId());
         }
 
-        // DETAILED level
-        if (projectionType == ProjectionType.DETAILED) {
-            return clinicalDataRepository.getSampleClinicalDataDetailed(studyIds, sampleIds, attributeIds);
-        }
-
-        // ID or SUMMARY level
-        List<ClinicalData> clinicalDataList = clinicalDataRepository.getSampleClinicalDataSummary(studyIds, sampleIds, attributeIds);
-        // ID level doesn't have attrValue
-        if (projectionType == ProjectionType.ID) {
-            for (ClinicalData clinicalData : clinicalDataList) {
-                clinicalData.setAttrValue(null);
-            }
-        }
-        return clinicalDataList;
+        return clinicalDataRepository.getSampleClinicalData(studyIds, sampleIds, attributeIds, projectionType);
     }
 }
 
diff --git a/...rtal/infrastructure/repository/clickhouse/clinical_data/ClickhouseClinicalDataMapper.java b/...rtal/infrastructure/repository/clickhouse/clinical_data/ClickhouseClinicalDataMapper.java
@@ -3,6 +3,7 @@
 import org.cbioportal.legacy.model.ClinicalData;
 import org.cbioportal.legacy.model.ClinicalDataCountItem;
 import org.cbioportal.domain.studyview.StudyViewFilterContext;
+import org.cbioportal.shared.enums.ProjectionType;
 
 import java.util.List;
 
@@ -31,9 +32,7 @@ public interface ClickhouseClinicalDataMapper {
      */
     List<ClinicalData> getSampleClinicalDataFromStudyViewFilter(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds);
 
-    List<ClinicalData> getSampleClinicalDataSummary(List<String> studyIds, List<String> sampleIds, List<String> attributeIds);
-
-    List<ClinicalData> getSampleClinicalDataDetailed(List<String> studyIds, List<String> sampleIds, List<String> attributeIds);
+    List<ClinicalData> getSampleClinicalData(List<String> studyIds, List<String> sampleIds, List<String> attributeIds, ProjectionType projectionType);
 
     /**
      * Retrieves patient clinical data based on the study view filter context and attribute IDs.
@@ -44,9 +43,7 @@ public interface ClickhouseClinicalDataMapper {
      */
     List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilterContext studyViewFilterContext, List<String> attributeIds);
 
-    List<ClinicalData> getPatientClinicalDataSummary(List<String> studyIds, List<String> patientIds, List<String> attributeIds);
-
-    List<ClinicalData> getPatientClinicalDataDetailed(List<String> studyIds, List<String> patientIds, List<String> attributeIds);
+    List<ClinicalData> getPatientClinicalData(List<String> studyIds, List<String> patientIds, List<String> attributeIds, ProjectionType projectionType);
 
 }
 
diff --git a/.../infrastructure/repository/clickhouse/clinical_data/ClickhouseClinicalDataRepository.java b/.../infrastructure/repository/clickhouse/clinical_data/ClickhouseClinicalDataRepository.java
@@ -4,6 +4,7 @@
 import org.cbioportal.legacy.model.ClinicalData;
 import org.cbioportal.legacy.model.ClinicalDataCountItem;
 import org.cbioportal.domain.studyview.StudyViewFilterContext;
+import org.cbioportal.shared.enums.ProjectionType;
 import org.springframework.context.annotation.Profile;
 import org.springframework.stereotype.Repository;
 
@@ -24,33 +25,23 @@ public ClickhouseClinicalDataRepository(ClickhouseClinicalDataMapper mapper) {
 
 
     @Override
-    public List<ClinicalData> getPatientClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes) {
+    public List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes) {
         return mapper.getPatientClinicalDataFromStudyViewFilter(studyViewFilterContext, filteredAttributes);
     }
 
     @Override
-    public List<ClinicalData> getPatientClinicalDataSummary(List<String> studyIds, List<String> patientIds, List<String> attributeIds) {
-        return mapper.getPatientClinicalDataSummary(studyIds, patientIds, attributeIds);
+    public List<ClinicalData> getPatientClinicalData(List<String> studyIds, List<String> patientIds, List<String> attributeIds, ProjectionType projectionType) {
+        return mapper.getPatientClinicalData(studyIds, patientIds, attributeIds, projectionType);
     }
 
     @Override
-    public List<ClinicalData> getPatientClinicalDataDetailed(List<String> studyIds, List<String> patientIds, List<String> attributeIds) {
-        return mapper.getPatientClinicalDataDetailed(studyIds, patientIds, attributeIds);
-    }
-
-    @Override
-    public List<ClinicalData> getSampleClinicalData(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes) {
+    public List<ClinicalData> getSampleClinicalDataFromStudyViewFilter(StudyViewFilterContext studyViewFilterContext, List<String> filteredAttributes) {
         return mapper.getSampleClinicalDataFromStudyViewFilter(studyViewFilterContext, filteredAttributes);
     }
 
     @Override
-    public List<ClinicalData> getSampleClinicalDataSummary(List<String> studyIds, List<String> sampleIds, List<String> attributeIds) {
-        return mapper.getSampleClinicalDataSummary(studyIds, sampleIds, attributeIds);
-    }
-
-    @Override
-    public List<ClinicalData> getSampleClinicalDataDetailed(List<String> studyIds, List<String> sampleIds, List<String> attributeIds) {
-        return mapper.getSampleClinicalDataDetailed(studyIds, sampleIds, attributeIds);
+    public List<ClinicalData> getSampleClinicalData(List<String> studyIds, List<String> sampleIds, List<String> attributeIds, ProjectionType projectionType) {
+        return mapper.getSampleClinicalData(studyIds, sampleIds, attributeIds, projectionType);
     }
 
     @Override

diff --git a/src/main/resources/mappers/clickhouse/clinical_data/ClickhouseClinicalDataMapper.xml b/src/main/resources/mappers/clickhouse/clinical_data/ClickhouseClinicalDataMapper.xml
@@ -45,6 +45,85 @@
         AND type = 'patient'
     </select>
 
+    <select id="getSampleClinicalData" resultMap="clinicalDataResultMap">
+        SELECT
+            cd.internal_id as internalId,
+            replaceOne(cd.sample_unique_id, concat(cd.cancer_study_identifier, '_'), '') as sampleId,
+            replaceOne(cd.patient_unique_id, concat(cd.cancer_study_identifier, '_'), '') as patientId,
+            cd.attribute_name as attrId,
+            <if test="projectionType != 'ID'">
+                cd.attribute_value as attrValue,
+            </if>
+            cd.cancer_study_identifier as studyId,
+            <if test="projectionType == 'DETAILED'">
+                cam.display_name as displayName,
+                cam.description,
+                cam.datatype,
+                cam.patient_attribute as patientAttribute,
+                cam.priority,
+                cam.cancer_study_id as cancerStudyId,
+            </if>
+        FROM clinical_data_derived cd
+        <if test="projectionType == 'DETAILED'">
+            LEFT JOIN cancer_study cs ON cd.cancer_study_identifier = cs.cancer_study_identifier
+            LEFT JOIN clinical_attribute_meta cam ON cd.attribute_name = cam.attr_id AND cs.cancer_study_id = cam.cancer_study_id
+        </if>
+        <where>
+            cd.type = 'sample'
+            <if test="sampleIds != null and !sampleIds.isEmpty()">
+                AND cd.sample_unique_id IN
+                <foreach index="i" collection="sampleIds" open="(" separator="," close=")">
+                    concat(#{studyIds[${i}]}, '_', #{sampleIds[${i}]})
+                </foreach>
+            </if>
+            <if test="attributeIds != null and !attributeIds.isEmpty()">
+                AND cd.attribute_name IN
+                <foreach item="attributeId" collection="attributeIds" open="(" separator="," close=")">
+                    #{attributeId}
+                </foreach>
+            </if>
+        </where>
+    </select>
+
+    <select id="getPatientClinicalData" resultMap="clinicalDataResultMap">
+        SELECT
+            cd.internal_id as internalId,
+            replaceOne(cd.patient_unique_id, concat(cd.cancer_study_identifier, '_'), '') as patientId,
+            cd.attribute_name as attrId,
+            <if test="projectionType != 'ID'">
+                cd.attribute_value as attrValue,
+            </if>
+            cd.cancer_study_identifier as studyId,
+            <if test="projectionType == 'DETAILED'">
+                cam.display_name as displayName,
+                cam.description,
+                cam.datatype,
+                cam.patient_attribute as patientAttribute,
+                cam.priority,
+                cam.cancer_study_id as cancerStudyId,
+            </if>
+        FROM clinical_data_derived cd
+        <if test="projectionType == 'DETAILED'">
+            LEFT JOIN cancer_study cs ON cd.cancer_study_identifier = cs.cancer_study_identifier
+            LEFT JOIN clinical_attribute_meta cam ON cd.attribute_name = cam.attr_id AND cs.cancer_study_id = cam.cancer_study_id
+        </if>
+        <where>
+            cd.type = 'patient'
+            <if test="patientIds != null and !patientIds.isEmpty()">
+                AND cd.patient_unique_id IN
+                <foreach index="i" collection="patientIds" open="(" separator="," close=")">
+                    concat(#{studyIds[${i}]}, '_', #{patientIds[${i}]})
+                </foreach>
+            </if>
+            <if test="attributeIds != null and !attributeIds.isEmpty()">
+                AND cd.attribute_name IN
+                <foreach item="attributeId" collection="attributeIds" open="(" separator="," close=")">
+                    #{attributeId}
+                </foreach>
+            </if>
+        </where>
+    </select>
+
     <!-- for /clinical-data-counts/fetch (returns ClinicalData) which will then be converted to clinicalDataCountItems -->
     <select id="getClinicalDataCounts" resultMap="ClinicalDataCountItemResultMap">
         <include refid="getClinicalDataCountsQuery">
@@ -111,7 +190,6 @@
         )
     </sql>
 
-
     <resultMap id="ClinicalDataCountItemResultMap" type="org.cbioportal.legacy.model.ClinicalDataCountItem">
         <result property="attributeId" column="attributeId"/>
         <collection property="counts" ofType="org.cbioportal.legacy.model.ClinicalDataCount">
@@ -120,4 +198,26 @@
             <result property="count" column="count"/>
         </collection>
     </resultMap>
+
+    <resultMap id="clinicalAttributeResultMap" type="org.cbioportal.legacy.model.ClinicalAttribute">
+        <id property="attrId" column="attrId"/>
+        <result property="displayName" column="displayName"/>
+        <result property="description" column="description"/>
+        <result property="datatype" column="datatype"/>
+        <result property="patientAttribute" column="patientAttribute"/>
+        <result property="priority" column="priority"/>
+        <result property="cancerStudyId" column="cancerStudyId"/>
+        <result property="cancerStudyIdentifier" column="studyId"/>
+    </resultMap>
+
+    <resultMap id="clinicalDataResultMap" type="org.cbioportal.legacy.model.ClinicalData">
+        <id property="internalId" column="internalId"/>
+        <result property="sampleId" column="sampleId"/>
+        <result property="patientId" column="patientId"/>
+        <result property="studyId" column="studyId"/>
+        <result property="attrId" column="attrId"/>
+        <result property="attrValue" column="attrValue"/>
+        <association property="clinicalAttribute" resultMap="clinicalAttributeResultMap"/>
+    </resultMap>
+
 </mapper>