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Rfc80/clinical event timeline endpoint (#10899)
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* Add Clinical Events Timeline counts endpoint

* Add comments for StudyViewFilter
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@haynescd
haynescd authored Jul 19, 2024
1 parent 3455f97 commit 77bf77f
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Showing 12 changed files with 271 additions and 90 deletions.
3 changes: 3 additions & 0 deletions src/main/java/org/cbioportal/persistence/StudyViewRepository.java
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Expand Up @@ -5,6 +5,7 @@
import org.cbioportal.model.CaseListDataCount;
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.ClinicalDataCount;
import org.cbioportal.model.ClinicalEventTypeCount;
import org.cbioportal.model.CopyNumberCountByGene;
import org.cbioportal.model.GenomicDataCount;
import org.cbioportal.model.Sample;
Expand Down Expand Up @@ -44,4 +45,6 @@ public interface StudyViewRepository {
Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, String alterationType);

int getTotalProfiledCountsByAlterationType(StudyViewFilter studyViewFilter, String alterationType);

List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter);
}
3 changes: 3 additions & 0 deletions src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
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Expand Up @@ -6,6 +6,7 @@
import org.cbioportal.model.ClinicalAttribute;
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.ClinicalDataCount;
import org.cbioportal.model.ClinicalEventTypeCount;
import org.cbioportal.model.CopyNumberCountByGene;
import org.cbioportal.model.GenePanelToGene;
import org.cbioportal.model.GenomicDataCount;
Expand Down Expand Up @@ -51,4 +52,6 @@ List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, C
List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);

int getTotalProfiledCountByAlterationType(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);

List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
}
41 changes: 26 additions & 15 deletions src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
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Expand Up @@ -4,6 +4,7 @@
import org.cbioportal.model.CaseListDataCount;
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.ClinicalDataCount;
import org.cbioportal.model.ClinicalEventTypeCount;
import org.cbioportal.model.GenePanelToGene;
import org.cbioportal.model.GenomicDataCount;
import org.cbioportal.model.CopyNumberCountByGene;
Expand Down Expand Up @@ -39,44 +40,46 @@ public StudyViewMyBatisRepository(StudyViewMapper mapper) {
@Override
public List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getFilteredSamples(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter));
return mapper.getFilteredSamples(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter));
}

@Override
public List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getMutatedGenes(studyViewFilter, categorizedClinicalDataCountFilter,
shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter),
AlterationFilterHelper.build(studyViewFilter.getAlterationFilter()));
}

@Override
public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getCnaGenes(studyViewFilter, categorizedClinicalDataCountFilter,
shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter),
AlterationFilterHelper.build(studyViewFilter.getAlterationFilter()));
}

@Override
public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getStructuralVariantGenes(studyViewFilter, categorizedClinicalDataCountFilter,
shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter),
AlterationFilterHelper.build(studyViewFilter.getAlterationFilter()));
}

@Override
public List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getClinicalDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
return mapper.getClinicalDataCounts(studyViewFilter, categorizedClinicalDataCountFilter,
shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter),
filteredAttributes, FILTERED_CLINICAL_ATTR_VALUES );
}

@Override
public List<GenomicDataCount> getGenomicDataCounts(StudyViewFilter studyViewFilter) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getGenomicDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter));
return mapper.getGenomicDataCounts(studyViewFilter, categorizedClinicalDataCountFilter,
shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter));
}

@Override
Expand Down Expand Up @@ -106,46 +109,47 @@ public Map<String, ClinicalDataType> getClinicalAttributeDatatypeMap() {
@Override
public List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getCaseListDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter));
return mapper.getCaseListDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter));
}


private boolean shouldApplyPatientIdFilters(CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
return categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters() != null && !categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters().isEmpty()
private boolean shouldApplyPatientIdFilters(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
return studyViewFilter.getClinicalEventFilters() != null && !studyViewFilter.getClinicalEventFilters().isEmpty()
|| categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters() != null && !categorizedClinicalDataCountFilter.getPatientCategoricalClinicalDataFilters().isEmpty()
|| categorizedClinicalDataCountFilter.getPatientNumericalClinicalDataFilters() != null && !categorizedClinicalDataCountFilter.getPatientNumericalClinicalDataFilters().isEmpty();
}

@Override
public List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getSampleClinicalDataFromStudyViewFilter(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), attributeIds);
return mapper.getSampleClinicalDataFromStudyViewFilter(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter), attributeIds);
}

@Override
public List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getPatientClinicalDataFromStudyViewFilter(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), attributeIds);
return mapper.getPatientClinicalDataFromStudyViewFilter(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter), attributeIds);
}

@Override
public Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, String alterationType) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getTotalProfiledCounts(studyViewFilter, categorizedClinicalDataCountFilter,
shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), alterationType);
shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter), alterationType);
}

@Override
public int getFilteredSamplesCount(StudyViewFilter studyViewFilter) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getFilteredSamplesCount(studyViewFilter, categorizedClinicalDataCountFilter,
shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter));
shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter));
}

@Override
public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, String alterationType) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getMatchingGenePanelIds(studyViewFilter, categorizedClinicalDataCountFilter,
shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), alterationType)
shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter), alterationType)
.stream()
.collect(Collectors.groupingBy(GenePanelToGene::getHugoGeneSymbol,
Collectors.mapping(GenePanelToGene::getGenePanelId, Collectors.toSet())));
Expand All @@ -155,7 +159,14 @@ public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilter studyVie
public int getTotalProfiledCountsByAlterationType(StudyViewFilter studyViewFilter, String alterationType) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getTotalProfiledCountByAlterationType(studyViewFilter, categorizedClinicalDataCountFilter,
shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), alterationType);
shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter), alterationType);
}

@Override
public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return mapper.getClinicalEventTypeCounts(studyViewFilter, categorizedClinicalDataCountFilter,
shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter));
}

private void buildClinicalAttributeNameMap() {
Expand Down
3 changes: 3 additions & 0 deletions src/main/java/org/cbioportal/service/StudyViewColumnarService.java
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Expand Up @@ -4,6 +4,7 @@
import org.cbioportal.model.CaseListDataCount;
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.ClinicalDataCountItem;
import org.cbioportal.model.ClinicalEventTypeCount;
import org.cbioportal.model.GenomicDataCount;
import org.cbioportal.model.CopyNumberCountByGene;
import org.cbioportal.model.Sample;
Expand Down Expand Up @@ -32,5 +33,7 @@ public interface StudyViewColumnarService {
List<ClinicalData> getSampleClinicalData(StudyViewFilter studyViewFilter, List<String> attributeIds);

List<GenomicDataCount> getGenomicDataCounts(StudyViewFilter studyViewFilter);

List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter);

}
8 changes: 7 additions & 1 deletion src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
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Expand Up @@ -5,6 +5,7 @@
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.GenomicDataCount;
import org.cbioportal.model.Sample;
Expand Down Expand Up @@ -50,7 +51,12 @@ public List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilt
public List<GenomicDataCount> getGenomicDataCounts(StudyViewFilter studyViewFilter) {
return studyViewRepository.getGenomicDataCounts(studyViewFilter);
}


@Override
public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter) {
return studyViewRepository.getClinicalEventTypeCounts(studyViewFilter);
}

public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter) {
return alterationCountService.getCnaGenes(studyViewFilter);
}
Expand Down
27 changes: 26 additions & 1 deletion src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
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Expand Up @@ -13,9 +13,10 @@
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.ClinicalDataBin;
import org.cbioportal.model.ClinicalDataCountItem;
import org.cbioportal.model.ClinicalEventTypeCount;
import org.cbioportal.model.ClinicalViolinPlotData;
import org.cbioportal.model.DensityPlotData;
import org.cbioportal.model.CopyNumberCountByGene;
import org.cbioportal.model.DensityPlotData;
import org.cbioportal.model.GenomicDataCount;
import org.cbioportal.model.Sample;
import org.cbioportal.service.ClinicalDataDensityPlotService;
Expand Down Expand Up @@ -325,4 +326,28 @@ public ResponseEntity<ClinicalViolinPlotData> fetchClinicalDataViolinPlots(

return new ResponseEntity<>(result, HttpStatus.OK);
}

@PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
@PostMapping(value = "/column-store/clinical-event-type-counts/fetch", consumes = MediaType.APPLICATION_JSON_VALUE,
produces = MediaType.APPLICATION_JSON_VALUE)
@Operation(description = "Get Counts of Clinical Event Types by Study View Filter")
@ApiResponse(responseCode = "200", description = "OK",
content = @Content(array = @ArraySchema(schema = @Schema(implementation = ClinicalEventTypeCount.class))))
public ResponseEntity<List<ClinicalEventTypeCount>> getClinicalEventTypeCounts(
@Parameter(required = true, description = "Study view filter")
@Valid
@RequestBody(required = false)
StudyViewFilter studyViewFilter,

@Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface
@RequestAttribute(required = false, value = "involvedCancerStudies")
Collection<String> involvedCancerStudies,

@Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above.
@Valid
@RequestAttribute(required = false, value = "interceptedStudyViewFilter")
StudyViewFilter interceptedStudyViewFilter
) {
return new ResponseEntity<>(studyViewColumnarService.getClinicalEventTypeCounts(interceptedStudyViewFilter), HttpStatus.OK);
}
}
29 changes: 29 additions & 0 deletions src/main/resources/db-scripts/clickhouse/clickhouse.sql
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Expand Up @@ -3,6 +3,7 @@ DROP TABLE IF EXISTS gene_panel_to_gene_derived;
DROP TABLE IF EXISTS sample_derived;
DROP TABLE IF EXISTS genomic_event_derived;
DROP TABLE IF EXISTS clinical_data_derived;
DROP TABLE IF EXISTS clinical_event_derived;


CREATE TABLE sample_to_gene_panel_derived
Expand Down Expand Up @@ -249,8 +250,36 @@ FROM patient AS p
ON (p.internal_id = clinpat.internal_id) AND (clinpat.attr_id = cam.attr_id)
WHERE cam.patient_attribute = 1;

CREATE TABLE clinical_event_derived
(
patient_unique_id String,
key String,
value String,
start_date Int32,
stop_date Int32 DEFAULT 0,
event_type LowCardinality(String),
cancer_study_identifier LowCardinality(String)
)
ENGINE = MergeTree
ORDER BY (event_type, patient_unique_id, cancer_study_identifier);

INSERT INTO clinical_event_derived
SELECT
concat(cs.cancer_study_identifier, '_', p.stable_id) AS patient_unique_id,
ced.key AS key,
ced.value AS value,
ce.start_date AS start_date,
ifNull(ce.stop_date, 0) AS stop_date,
ce.event_type AS event_type,
cs.cancer_study_identifier
FROM clinical_event ce
LEFT JOIN clinical_event_data ced ON ce.clinical_event_id = ced.clinical_event_id
INNER JOIN patient p ON ce.patient_id = p.internal_id
INNER JOIN cancer_study cs ON p.cancer_study_id = cs.cancer_study_id;

OPTIMIZE TABLE sample_to_gene_panel_derived;
OPTIMIZE TABLE gene_panel_to_gene_derived;
OPTIMIZE TABLE sample_derived;
OPTIMIZE TABLE genomic_event_derived;
OPTIMIZE TABLE clinical_data_derived;
OPTIMIZE TABLE clinical_event_derived;
18 changes: 18 additions & 0 deletions src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
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Expand Up @@ -109,6 +109,20 @@
</trim>
</sql>

<sql id="applyClinicalEventTypeFilter">
<foreach item="clinicalEventFilter" collection="studyViewFilter.getClinicalEventFilters()" open="INTERSECT"
separator="INTERSECT">
SELECT patient_unique_id
FROM clinical_event_derived
<where>
<foreach item="dataFilterValue" collection="clinicalEventFilter.values" open="(" separator=") OR ("
close=")">
event_type = '${dataFilterValue.value}'
</foreach>
</where>
</foreach>
</sql>

<sql id="patientUniqueIdsFromStudyViewFilter">
<trim prefixOverrides="INTERSECT">
<if test="categorizedClinicalDataCountFilter.getPatientNumericalClinicalDataFilters() != null and !categorizedClinicalDataCountFilter.getPatientNumericalClinicalDataFilters().isEmpty()">
Expand All @@ -129,6 +143,10 @@
</include>
</foreach>
</if>
<!-- Clinical Event Filter -->
<if test="studyViewFilter.clinicalEventFilters != null and !studyViewFilter.clinicalEventFilters.isEmpty()">
<include refid="applyClinicalEventTypeFilter"/>
</if>
</trim>
</sql>

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