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Merged
merged 2 commits into from
Nov 21, 2025
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Merged

Optimize clinical event derived queries #11813

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17828dd
optimize clinical event derived table related queries
onursumer Nov 17, 2025
2963ad2
add more sample treatment tests
onursumer Nov 18, 2025
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2 changes: 1 addition & 1 deletion src/main/resources/db-scripts/clickhouse/clickhouse.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -364,7 +364,7 @@ CREATE TABLE clinical_event_derived
cancer_study_identifier LowCardinality(String)
)
ENGINE = MergeTree
ORDER BY (event_type, patient_unique_id, cancer_study_identifier);
ORDER BY (cancer_study_identifier, event_type, patient_unique_id);

INSERT INTO clinical_event_derived
SELECT
Expand Down
48 changes: 40 additions & 8 deletions src/main/resources/mappers/clickhouse/studyview/ClickhouseStudyViewFilterMapper.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -190,8 +190,15 @@
ced.cancer_study_identifier AS cancer_study_identifier
FROM clinical_event_derived ced
<where>
key = 'SAMPLE_ID'
AND (event_type ILIKE 'Sample Acquisition' OR event_type ILIKE 'SPECIMEN')
<if test="studyViewFilterContext.customDataFilterCancerStudies != null and !studyViewFilterContext.customDataFilterCancerStudies.isEmpty()">
cancer_study_identifier IN
<foreach item="studyId" collection="studyViewFilterContext.customDataFilterCancerStudies" open="(" separator="," close=")">
#{studyId}
</foreach>
AND
</if>
(event_type ILIKE 'Sample Acquisition' OR event_type ILIKE 'SPECIMEN')
AND key = 'SAMPLE_ID'
</where>
GROUP BY patient_unique_id, ced.value, cancer_study_identifier
) ced
Expand All @@ -202,8 +209,16 @@
value AS treatment,
argMin(start_date, start_date) AS treatment_time_taken
FROM clinical_event_derived
WHERE lower(event_type) = 'treatment'
AND key = 'AGENT'
WHERE
<if test="studyViewFilterContext.customDataFilterCancerStudies != null and !studyViewFilterContext.customDataFilterCancerStudies.isEmpty()">
cancer_study_identifier IN
<foreach item="studyId" collection="studyViewFilterContext.customDataFilterCancerStudies" open="(" separator="," close=")">
#{studyId}
</foreach>
AND
</if>
lower(event_type) = 'treatment'
AND key = 'AGENT'
GROUP BY patient_unique_id, value
) ced_inner ON ced_inner.patient_unique_id = ced.patient_unique_id
<where>
Expand Down Expand Up @@ -232,7 +247,14 @@
SELECT patient_unique_id
FROM clinical_event_derived
<where>
<foreach item="dataFilterValue" collection="clinicalEventFilter.values" open="(" separator=") OR (" close=")">
<if test="studyViewFilterContext.customDataFilterCancerStudies != null and !studyViewFilterContext.customDataFilterCancerStudies.isEmpty()">
cancer_study_identifier IN
<foreach item="studyId" collection="studyViewFilterContext.customDataFilterCancerStudies" open="(" separator="," close=")">
#{studyId}
</foreach>
AND
</if>
<foreach item="dataFilterValue" collection="clinicalEventFilter.values" open="((" separator=") OR (" close="))">
event_type = #{dataFilterValue.value}
</foreach>
</where>
Expand All @@ -250,9 +272,19 @@
SELECT patient_unique_id
FROM clinical_event_derived
<where>
<foreach item="patientTreatmentFilter" collection="andedPatientTreatmentFilters.getFilters()" open="("
separator=") OR ("
close=")"> lower(event_type) = 'treatment'
<if test="studyViewFilterContext.customDataFilterCancerStudies != null and !studyViewFilterContext.customDataFilterCancerStudies.isEmpty()">
cancer_study_identifier IN
<foreach item="studyId" collection="studyViewFilterContext.customDataFilterCancerStudies" open="(" separator="," close=")">
#{studyId}
</foreach>
AND
</if>
<foreach
item="patientTreatmentFilter"
collection="andedPatientTreatmentFilters.getFilters()"
open="((" separator=") OR (" close="))"
>
lower(event_type) = 'treatment'
AND key = 'AGENT'
AND value = #{patientTreatmentFilter.treatment}
</foreach>
Expand Down
48 changes: 45 additions & 3 deletions src/main/resources/mappers/clickhouse/treatment/ClickhouseTreatmentMapper.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,13 @@
count(DISTINCT patient_unique_id) AS count
FROM clinical_event_derived
<where>
<if test="studyViewFilterContext.customDataFilterCancerStudies != null and !studyViewFilterContext.customDataFilterCancerStudies.isEmpty()">
cancer_study_identifier IN
<foreach item="studyId" collection="studyViewFilterContext.customDataFilterCancerStudies" open="(" separator="," close=")">
#{studyId}
</foreach>
AND
</if>
lower(event_type) = 'treatment'
AND key = 'AGENT'
AND
Expand All @@ -34,6 +41,13 @@
patient_unique_id
FROM clinical_event_derived
<where>
<if test="studyViewFilterContext.customDataFilterCancerStudies != null and !studyViewFilterContext.customDataFilterCancerStudies.isEmpty()">
cancer_study_identifier IN
<foreach item="studyId" collection="studyViewFilterContext.customDataFilterCancerStudies" open="(" separator="," close=")">
#{studyId}
</foreach>
AND
</if>
lower(event_type) = 'treatment'
AND key = 'AGENT'
AND
Expand All @@ -48,8 +62,15 @@
count(distinct ced.value) AS totalSamples
FROM clinical_event_derived ced
<where>
<if test="studyViewFilterContext.customDataFilterCancerStudies != null and !studyViewFilterContext.customDataFilterCancerStudies.isEmpty()">
cancer_study_identifier IN
<foreach item="studyId" collection="studyViewFilterContext.customDataFilterCancerStudies" open="(" separator="," close=")">
#{studyId}
</foreach>
AND
</if>
(event_type ILIKE 'Sample Acquisition' OR event_type ILIKE 'SPECIMEN')
AND key = 'SAMPLE_ID'
AND (event_type ILIKE 'Sample Acquisition' OR event_type ILIKE 'SPECIMEN')
AND
concat(ced.cancer_study_identifier, '_', ced.value) IN ( <include refid="org.cbioportal.infrastructure.repository.clickhouse.studyview.ClickhouseStudyViewFilterMapper.sampleUniqueIdsFromStudyViewFilter"/>)
AND
Expand All @@ -58,6 +79,13 @@
patient_unique_id
FROM clinical_event_derived
<where>
<if test="studyViewFilterContext.customDataFilterCancerStudies != null and !studyViewFilterContext.customDataFilterCancerStudies.isEmpty()">
cancer_study_identifier IN
<foreach item="studyId" collection="studyViewFilterContext.customDataFilterCancerStudies" open="(" separator="," close=")">
#{studyId}
</foreach>
AND
</if>
lower(event_type) = 'treatment'
AND key = 'AGENT'
AND
Expand Down Expand Up @@ -85,8 +113,15 @@
ced.cancer_study_identifier AS cancer_study_identifier
FROM clinical_event_derived ced
<where>
key = 'SAMPLE_ID'
AND (event_type ILIKE 'Sample Acquisition' OR event_type ILIKE 'SPECIMEN')
<if test="studyViewFilterContext.customDataFilterCancerStudies != null and !studyViewFilterContext.customDataFilterCancerStudies.isEmpty()">
cancer_study_identifier IN
<foreach item="studyId" collection="studyViewFilterContext.customDataFilterCancerStudies" open="(" separator="," close=")">
#{studyId}
</foreach>
AND
</if>
(event_type ILIKE 'Sample Acquisition' OR event_type ILIKE 'SPECIMEN')
AND key = 'SAMPLE_ID'
</where>
GROUP BY patient_unique_id, ced.value, cancer_study_identifier
</sql>
Expand All @@ -98,6 +133,13 @@
argMin(start_date, start_date) AS treatment_time_taken
FROM clinical_event_derived
<where>
<if test="studyViewFilterContext.customDataFilterCancerStudies != null and !studyViewFilterContext.customDataFilterCancerStudies.isEmpty()">
cancer_study_identifier IN
<foreach item="studyId" collection="studyViewFilterContext.customDataFilterCancerStudies" open="(" separator="," close=")">
#{studyId}
</foreach>
AND
</if>
lower(event_type) = 'treatment'
AND key = 'AGENT'
</where>
Expand Down
34 changes: 34 additions & 0 deletions ...oportal/infrastructure/repository/clickhouse/treatment/ClickhouseTreatmentMapperTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,8 @@ public void getPatientTreatments() {

@Test
public void getTotalSampleTreatmentCounts() {
// sample treatment counts without sample treatment filters

StudyViewFilter studyViewFilter = new StudyViewFilter();
studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));

Expand Down Expand Up @@ -126,6 +128,9 @@ public void getTotalSampleTreatmentCounts() {
.getTimeTaken()
.intValue());

// sample treatment counts with sample treatment filters

// PRE treatment test
SampleTreatmentFilter filter = new SampleTreatmentFilter();
filter.setTreatment("madeupanib");
filter.setTime(TemporalRelation.Pre);
Expand Down Expand Up @@ -155,5 +160,34 @@ public void getTotalSampleTreatmentCounts() {
assertEquals(0, totalSampleTreatmentCount);
assertEquals(0, sampleTreatmentCounts.size());
assertEquals(0, sampleTreatmentCountsWithSampleLists.size());

// POST treatment test
filter.setTime(TemporalRelation.Post);

totalSampleTreatmentCount =
mapper.getTotalSampleTreatmentCounts(
StudyViewFilterFactory.make(
studyViewFilter, null, studyViewFilter.getStudyIds(), null));

sampleTreatmentCounts =
mapper.getSampleTreatmentCounts(
StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
ProjectionType.SUMMARY.name());

sampleTreatmentCountsWithSampleLists =
mapper.getSampleTreatmentCounts(
StudyViewFilterFactory.make(studyViewFilter, null, studyViewFilter.getStudyIds(), null),
ProjectionType.DETAILED.name());

assertEquals(1, totalSampleTreatmentCount);
assertEquals(1, sampleTreatmentCounts.size());
assertEquals(1, sampleTreatmentCountsWithSampleLists.size());
assertEquals("madeupanib", sampleTreatmentCounts.getFirst().treatment());
assertEquals(1, sampleTreatmentCounts.getFirst().postSampleCount());
assertEquals(0, sampleTreatmentCounts.getFirst().preSampleCount());
assertEquals(1, sampleTreatmentCountsWithSampleLists.getFirst().postSampleCount());
assertEquals(0, sampleTreatmentCountsWithSampleLists.getFirst().preSampleCount());
assertEquals(1, sampleTreatmentCountsWithSampleLists.getFirst().postSamples().size());
assertEquals(0, sampleTreatmentCountsWithSampleLists.getFirst().preSamples().size());
}
}
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