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✨ Add StructuralVariant-genes endpoint #10854

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Jun 24, 2024
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✨ Add StructuralVariant-genes endpoint #10854

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7bcf5bb
:sparkles: Add StructuralVariant-genes endpoint
haynescd Jun 21, 2024
fc9f935
Fix sonar issues
haynescd Jun 21, 2024
c6fcfdd
Update MatchingGenePanel request to return list
haynescd Jun 21, 2024
9d8461f
Create and use sample_derive
haynescd Jun 21, 2024
36d6626
Update where sample_derived is stored to fix unit test
haynescd Jun 21, 2024
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6 changes: 4 additions & 2 deletions src/main/java/org/cbioportal/persistence/StudyViewRepository.java
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Expand Up @@ -3,8 +3,8 @@
import org.cbioportal.model.AlterationCountByGene;
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.ClinicalDataCount;
import org.cbioportal.model.GenomicDataCount;
import org.cbioportal.model.CopyNumberCountByGene;
import org.cbioportal.model.GenomicDataCount;
import org.cbioportal.model.Sample;
import org.cbioportal.persistence.enums.ClinicalAttributeDataSource;
import org.cbioportal.persistence.enums.ClinicalAttributeDataType;
Expand All @@ -13,6 +13,7 @@

import java.util.List;
import java.util.Map;
import java.util.Set;

public interface StudyViewRepository {
List<Sample> getFilteredSamples(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
Expand All @@ -24,6 +25,7 @@ public interface StudyViewRepository {
List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);

List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);

List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes);

Expand All @@ -39,7 +41,7 @@ public interface StudyViewRepository {

int getFilteredSamplesCount(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);

Map<String, AlterationCountByGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType);
Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType);

int getTotalProfiledCountsByAlterationType(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType);
}
6 changes: 4 additions & 2 deletions src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
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Expand Up @@ -24,6 +24,9 @@ List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, Cat

List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
boolean applyPatientIdFilters, AlterationFilterHelper alterationFilterHelper);

List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
boolean applyPatientIdFilters, AlterationFilterHelper alterationFilterHelper);

List<ClinicalDataCount> getPatientClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
boolean applyPatientIdFilters, List<String> attributeIds, List<String> filteredAttributeValues);
Expand All @@ -45,8 +48,7 @@ List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, C

int getFilteredSamplesCount(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);

@MapKey("hugoGeneSymbol")
Map<String, AlterationCountByGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);

int getTotalProfiledCountByAlterationType(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
}
17 changes: 15 additions & 2 deletions src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
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Expand Up @@ -2,6 +2,7 @@
import org.cbioportal.model.AlterationCountByGene;
import org.cbioportal.model.ClinicalData;
import org.cbioportal.model.ClinicalDataCount;
import org.cbioportal.model.GenePanelToGene;
import org.cbioportal.model.GenomicDataCount;
import org.cbioportal.model.CopyNumberCountByGene;
import org.cbioportal.model.Sample;
Expand All @@ -16,6 +17,8 @@
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;

@Repository
public class StudyViewMyBatisRepository implements StudyViewRepository {
Expand Down Expand Up @@ -47,6 +50,13 @@ public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter,
AlterationFilterHelper.build(studyViewFilter.getAlterationFilter()));
}

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

@Override
public List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<String> filteredAttributes) {
return mapper.getClinicalDataCounts(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter),
Expand Down Expand Up @@ -103,9 +113,12 @@ public int getFilteredSamplesCount(StudyViewFilter studyViewFilter, CategorizedC
}

@Override
public Map<String, AlterationCountByGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType) {
public Map<String, Set<String>> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, String alterationType) {
return mapper.getMatchingGenePanelIds(studyViewFilter, categorizedClinicalDataCountFilter,
shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), alterationType);
shouldApplyPatientIdFilters(categorizedClinicalDataCountFilter), alterationType)
.stream()
.collect(Collectors.groupingBy(GenePanelToGene::getHugoGeneSymbol,
Collectors.mapping(GenePanelToGene::getGenePanelId, Collectors.toSet())));
}

@Override
Expand Down
39 changes: 0 additions & 39 deletions ...ava/org/cbioportal/persistence/mybatisclickhouse/typehandler/GenePanelIdsTypeHandler.java
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This file was deleted.

2 changes: 2 additions & 0 deletions src/main/java/org/cbioportal/service/AlterationCountService.java
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Expand Up @@ -80,4 +80,6 @@ Pair<List<CopyNumberCountByGene>, Long> getPatientCnaGeneCounts(List<MolecularPr
List<AlterationCountByGene> getMutatedGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);
List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);

List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter);

}
1 change: 1 addition & 0 deletions src/main/java/org/cbioportal/service/StudyViewColumnarService.java
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Expand Up @@ -16,6 +16,7 @@ public interface StudyViewColumnarService {

List<AlterationCountByGene> getMutatedGenes(StudyViewFilter interceptedStudyViewFilter);
List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter interceptedStudyViewFilter);
List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter);

List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes);

Expand Down
16 changes: 11 additions & 5 deletions src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
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Expand Up @@ -265,7 +265,13 @@ public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter,
var copyNumberCountByGenes = studyViewRepository.getCnaGenes(studyViewFilter, categorizedClinicalDataCountFilter);
return populateAlterationCounts(copyNumberCountByGenes, studyViewFilter, categorizedClinicalDataCountFilter, AlterationType.COPY_NUMBER_ALTERATION);
}


@Override
public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter) {
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var alterationCountByGenes = studyViewRepository.getStructuralVariantGenes(studyViewFilter, categorizedClinicalDataCountFilter);
return populateAlterationCounts(alterationCountByGenes, studyViewFilter, categorizedClinicalDataCountFilter, AlterationType.STRUCTURAL_VARIANT);
}

private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@NonNull List<T> alterationCounts,
@NonNull StudyViewFilter studyViewFilter,
@NonNull CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter,
Expand All @@ -276,13 +282,13 @@ private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@Non
alterationType.toString());
var profiledCountWithoutGenePanelData = studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilter, categorizedClinicalDataCountFilter, alterationType.toString());
var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilter,
categorizedClinicalDataCountFilter, AlterationType.MUTATION_EXTENDED.toString());
categorizedClinicalDataCountFilter, alterationType.toString());

updatedAlterationCounts
updatedAlterationCounts.parallelStream()
.forEach(alterationCountByGene -> {
String hugoGeneSymbol = alterationCountByGene.getHugoGeneSymbol();
var matchingGenePanelIds = matchingGenePanelIdsMap.get(hugoGeneSymbol) != null ?
matchingGenePanelIdsMap.get(hugoGeneSymbol).getMatchingGenePanelIds() : null;
Set<String> matchingGenePanelIds = matchingGenePanelIdsMap.get(hugoGeneSymbol) != null ?
matchingGenePanelIdsMap.get(hugoGeneSymbol) : Collections.emptySet();

int totalProfiledCount = getTotalProfiledCount(alterationCountByGene.getHugoGeneSymbol(),
profiledCountsMap, profiledCountWithoutGenePanelData, matchingGenePanelIds);
Expand Down
6 changes: 6 additions & 0 deletions src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
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Expand Up @@ -61,6 +61,12 @@ public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter)
return alterationCountService.getCnaGenes(studyViewFilter, categorizedClinicalDataCountFilter);
}

@Override
public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter studyViewFilter) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
return alterationCountService.getStructuralVariantGenes(studyViewFilter, categorizedClinicalDataCountFilter);
}

@Override
public List<ClinicalDataCountItem> getClinicalDataCounts(StudyViewFilter studyViewFilter, List<String> filteredAttributes) {
CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
Expand Down
16 changes: 16 additions & 0 deletions src/main/java/org/cbioportal/web/columnar/StudyViewColumnStoreController.java
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Expand Up @@ -132,6 +132,22 @@ public ResponseEntity<List<CopyNumberCountByGene>> fetchCnaGenes(
);
}

@PostMapping(value = "/column-store/structuralvariant-genes/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
@Operation(description = "Fetch structural variant genes by study view filter")
@ApiResponse(responseCode = "200", description = "OK",
content = @Content(array = @ArraySchema(schema = @Schema(implementation = AlterationCountByGene.class))))
public ResponseEntity<List<AlterationCountByGene>> fetchStructuralVariantGenes(
@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. This attribute is needed for the @PreAuthorize tag above.
@RequestAttribute(required = false, value = "involvedCancerStudies") Collection<String> involvedCancerStudies,
@Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface.
@Valid @RequestAttribute(required = false, value = "interceptedStudyViewFilter") StudyViewFilter interceptedStudyViewFilter
) {
return new ResponseEntity<>(studyViewColumnarService.getStructuralVariantGenes(interceptedStudyViewFilter), HttpStatus.OK);
}

@PreAuthorize("hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.utils.security.AccessLevel).READ)")
@PostMapping(value = "/column-store/clinical-data-counts/fetch",
consumes = MediaType.APPLICATION_JSON_VALUE, produces = MediaType.APPLICATION_JSON_VALUE)
Expand Down
16 changes: 15 additions & 1 deletion src/main/resources/db-scripts/clickhouse/clickhouse.sql
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Expand Up @@ -35,4 +35,18 @@ CREATE TABLE gene_panel_to_gene
gene_panel_id LowCardinality(String),
gene String
) ENGINE = MergeTree()
ORDER BY (gene_panel_id);
ORDER BY (gene_panel_id);

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CREATE TABLE sample_derived
(
sample_unique_id String,
sample_unique_id_base64 String,
sample_stable_id String,
patient_unique_id String,
patient_unique_id_base64 String,
patient_stable_id String,
cancer_study_identifier LowCardinality(String),
internal_id Int
)
ENGINE = MergeTree
ORDER BY (cancer_study_identifier, sample_unique_id);
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