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test check
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@Djokovic0311
Djokovic0311 committed Aug 13, 2023
1 parent ddcf44e commit 38911ab
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Showing 8 changed files with 65 additions and 295 deletions.
2 changes: 1 addition & 1 deletion service/src/main/java/org/cbioportal/service/ExpressionEnrichmentService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ List<GenomicEnrichment> getGenomicEnrichments(String molecularProfileId,
Map<String, List<MolecularProfileCaseIdentifier>> molecularProfileCaseSets, EnrichmentType enrichmentType)
throws MolecularProfileNotFoundException;

List<GenericAssayEnrichment> getGenericAssayEnrichments(String molecularProfileId,
List<GenericAssayEnrichment> getGenericAssayNumericalEnrichments(String molecularProfileId,
Map<String, List<MolecularProfileCaseIdentifier>> molecularProfileCaseSets, EnrichmentType enrichmentType)
throws MolecularProfileNotFoundException;
List<GenericAssayBinaryEnrichment> getGenericAssayBinaryEnrichments(
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23 changes: 0 additions & 23 deletions service/src/main/java/org/cbioportal/service/GenericAssayEnrichmentService.java
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131 changes: 56 additions & 75 deletions service/src/main/java/org/cbioportal/service/impl/ExpressionEnrichmentServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,19 @@
import java.util.stream.Collectors;

import org.apache.commons.lang3.BooleanUtils;
import org.cbioportal.model.*;
import org.cbioportal.model.MolecularProfile.MolecularAlterationType;
import org.cbioportal.model.meta.GenericAssayMeta;
import org.cbioportal.model.EnrichmentType;
import org.cbioportal.model.GenericAssayBinaryEnrichment;
import org.cbioportal.model.GenericAssayCategoricalEnrichment;
import org.cbioportal.model.GenericAssayMolecularAlteration;
import org.cbioportal.model.MolecularProfileCaseIdentifier;
import org.cbioportal.model.MolecularProfile;
import org.cbioportal.model.Sample;
import org.cbioportal.model.GenericAssayEnrichment;
import org.cbioportal.model.GenomicEnrichment;
import org.cbioportal.model.Gene;
import org.cbioportal.model.GeneMolecularAlteration;
import org.cbioportal.persistence.MolecularDataRepository;
import org.cbioportal.service.ExpressionEnrichmentService;
import org.cbioportal.service.GeneService;
Expand Down Expand Up @@ -43,62 +53,49 @@ public class ExpressionEnrichmentServiceImpl implements ExpressionEnrichmentServ
// molecularDataService in fetchCoExpressions
@Transactional(readOnly = true)
public List<GenomicEnrichment> getGenomicEnrichments(String molecularProfileId,
Map<String, List<MolecularProfileCaseIdentifier>> molecularProfileCaseSets, EnrichmentType enrichmentType)
throws MolecularProfileNotFoundException {

Map<String, List<MolecularProfileCaseIdentifier>> molecularProfileCaseSets, EnrichmentType enrichmentType)
throws MolecularProfileNotFoundException {
MolecularProfile molecularProfile = molecularProfileService.getMolecularProfile(molecularProfileId);

List<MolecularAlterationType> validGenomicMolecularAlterationTypes = Arrays.asList(
MolecularAlterationType.MICRO_RNA_EXPRESSION, MolecularAlterationType.MRNA_EXPRESSION,
MolecularAlterationType.MRNA_EXPRESSION_NORMALS, MolecularAlterationType.RNA_EXPRESSION,
MolecularAlterationType.METHYLATION, MolecularAlterationType.METHYLATION_BINARY,
MolecularAlterationType.PHOSPHORYLATION, MolecularAlterationType.PROTEIN_LEVEL,
MolecularAlterationType.PROTEIN_ARRAY_PROTEIN_LEVEL,
MolecularAlterationType.PROTEIN_ARRAY_PHOSPHORYLATION);

MolecularAlterationType.MICRO_RNA_EXPRESSION, MolecularAlterationType.MRNA_EXPRESSION,
MolecularAlterationType.MRNA_EXPRESSION_NORMALS, MolecularAlterationType.RNA_EXPRESSION,
MolecularAlterationType.METHYLATION, MolecularAlterationType.METHYLATION_BINARY,
MolecularAlterationType.PHOSPHORYLATION, MolecularAlterationType.PROTEIN_LEVEL,
MolecularAlterationType.PROTEIN_ARRAY_PROTEIN_LEVEL,
MolecularAlterationType.PROTEIN_ARRAY_PHOSPHORYLATION);
validateMolecularProfile(molecularProfile, validGenomicMolecularAlterationTypes);

Iterable<GeneMolecularAlteration> maItr = molecularDataRepository
.getGeneMolecularAlterationsIterableFast(molecularProfile.getStableId());

.getGeneMolecularAlterationsIterableFast(molecularProfile.getStableId());
List<GenomicEnrichment> expressionEnrichments = expressionEnrichmentUtil.getEnrichments(molecularProfile,
molecularProfileCaseSets, enrichmentType, maItr);

molecularProfileCaseSets, enrichmentType, maItr);
List<Integer> entrezGeneIds = expressionEnrichments.stream().map(GenomicEnrichment::getEntrezGeneId)
.collect(Collectors.toList());

.collect(Collectors.toList());
Map<Integer, List<Gene>> geneMapByEntrezId = geneService
.fetchGenes(entrezGeneIds.stream().map(Object::toString).collect(Collectors.toList()), "ENTREZ_GENE_ID",
"SUMMARY")
.stream().collect(Collectors.groupingBy(Gene::getEntrezGeneId));

.fetchGenes(entrezGeneIds.stream().map(Object::toString).collect(Collectors.toList()), "ENTREZ_GENE_ID",
"SUMMARY")
.stream().collect(Collectors.groupingBy(Gene::getEntrezGeneId));
return expressionEnrichments.stream()
// filter Enrichments having no gene reference object(this
// happens when multiple
// entrez ids map to same hugo gene symbol)
.filter(expressionEnrichment -> geneMapByEntrezId.containsKey(expressionEnrichment.getEntrezGeneId()))
.map(expressionEnrichment -> {
Gene gene = geneMapByEntrezId.get(expressionEnrichment.getEntrezGeneId()).get(0);
expressionEnrichment.setHugoGeneSymbol(gene.getHugoGeneSymbol());
return expressionEnrichment;
}).collect(Collectors.toList());
// filter Enrichments having no gene reference object(this
// happens when multiple
// entrez ids map to same hugo gene symbol)
.filter(expressionEnrichment -> geneMapByEntrezId.containsKey(expressionEnrichment.getEntrezGeneId()))
.map(expressionEnrichment -> {
Gene gene = geneMapByEntrezId.get(expressionEnrichment.getEntrezGeneId()).get(0);
expressionEnrichment.setHugoGeneSymbol(gene.getHugoGeneSymbol());
return expressionEnrichment;
}).collect(Collectors.toList());
}

@Override
// transaction needs to be setup here in order to return Iterable from
// molecularDataRepository in getGenericAssayMolecularAlterationsIterable
@Transactional(readOnly = true)
public List<GenericAssayEnrichment> getGenericAssayEnrichments(String molecularProfileId,
Map<String, List<MolecularProfileCaseIdentifier>> molecularProfileCaseSets, EnrichmentType enrichmentType)
throws MolecularProfileNotFoundException {

Map<String, List<MolecularProfileCaseIdentifier>> molecularProfileCaseSets, EnrichmentType enrichmentType)
throws MolecularProfileNotFoundException {
MolecularProfile molecularProfile = molecularProfileService.getMolecularProfile(molecularProfileId);

validateMolecularProfile(molecularProfile, Arrays.asList(MolecularAlterationType.GENERIC_ASSAY));

Iterable<GenericAssayMolecularAlteration> maItr = molecularDataRepository
.getGenericAssayMolecularAlterationsIterable(molecularProfile.getStableId(), null, "SUMMARY");

.getGenericAssayMolecularAlterationsIterable(molecularProfile.getStableId(), null, "SUMMARY");
Map<String, List<MolecularProfileCaseIdentifier>> filteredMolecularProfileCaseSets;
if (BooleanUtils.isTrue(molecularProfile.getPatientLevel())) {
// Build sampleIdToPatientIdMap to quick find if a sample has shared patientId with other samples
Expand All @@ -120,34 +117,25 @@ public List<GenericAssayEnrichment> getGenericAssayEnrichments(String molecularP
filteredMolecularProfileCaseSets.put(pair.getKey(), identifierListUniqueByPatientId);
}
} else {
filteredMolecularProfileCaseSets = molecularProfileCaseSets;
filteredMolecularProfileCaseSets = molecularProfileCaseSets;
}
List<GenericAssayEnrichment> genericAssayEnrichments = expressionEnrichmentUtil.getEnrichments(molecularProfile,
filteredMolecularProfileCaseSets, enrichmentType, maItr);
filteredMolecularProfileCaseSets, enrichmentType, maItr);
List<String> getGenericAssayStableIds = genericAssayEnrichments.stream()
.map(GenericAssayEnrichment::getStableId).collect(Collectors.toList());
.map(GenericAssayEnrichment::getStableId).collect(Collectors.toList());
Map<String, GenericAssayMeta> genericAssayMetaByStableId = genericAssayService
.getGenericAssayMetaByStableIdsAndMolecularIds(getGenericAssayStableIds,
getGenericAssayStableIds.stream().map(stableId -> molecularProfileId)
.collect(Collectors.toList()),
"SUMMARY")
.stream().collect(Collectors.toMap(GenericAssayMeta::getStableId, Function.identity()));
.getGenericAssayMetaByStableIdsAndMolecularIds(getGenericAssayStableIds,
getGenericAssayStableIds.stream().map(stableId -> molecularProfileId)
.collect(Collectors.toList()),
"SUMMARY")
.stream().collect(Collectors.toMap(GenericAssayMeta::getStableId, Function.identity()));
return genericAssayEnrichments.stream().map(enrichmentDatum -> {
enrichmentDatum.setGenericEntityMetaProperties(
genericAssayMetaByStableId.get(enrichmentDatum.getStableId()).getGenericEntityMetaProperties());
genericAssayMetaByStableId.get(enrichmentDatum.getStableId()).getGenericEntityMetaProperties());
return enrichmentDatum;
}).collect(Collectors.toList());
}


private void validateMolecularProfile(MolecularProfile molecularProfile,
List<MolecularAlterationType> validMolecularAlterationTypes) throws MolecularProfileNotFoundException {
if (!validMolecularAlterationTypes.contains(molecularProfile.getMolecularAlterationType())) {
throw new MolecularProfileNotFoundException(molecularProfile.getStableId());
}
}


@Override
@Transactional(readOnly = true)
public List<GenericAssayBinaryEnrichment> getGenericAssayBinaryEnrichments(
Expand All @@ -156,7 +144,7 @@ public List<GenericAssayBinaryEnrichment> getGenericAssayBinaryEnrichments(
throws MolecularProfileNotFoundException {

// Validate and fetch molecular profile
MolecularProfile molecularProfile = getAndValidateMolecularProfile(molecularProfileId, true);
MolecularProfile molecularProfile = getAndValidateMolecularProfile(molecularProfileId, "BINARY");

// Get the molecular alterations for the provided profile
Iterable<GenericAssayMolecularAlteration> maItr = molecularDataRepository
Expand Down Expand Up @@ -193,13 +181,12 @@ public List<GenericAssayCategoricalEnrichment> getGenericAssayCategoricalEnrichm
Map<String, List<MolecularProfileCaseIdentifier>> molecularProfileCaseSets, EnrichmentType enrichmentType)
throws MolecularProfileNotFoundException {

MolecularProfile molecularProfile = getAndValidateMolecularProfile(molecularProfileId, false);
MolecularProfile molecularProfile = getAndValidateMolecularProfile(molecularProfileId, "CATEGORICAL");

Iterable<GenericAssayMolecularAlteration> maItr = molecularDataRepository
.getGenericAssayMolecularAlterationsIterable(molecularProfile.getStableId(), null, "SUMMARY");

Map<String, List<MolecularProfileCaseIdentifier>> filteredMolecularProfileCaseSets;
filteredMolecularProfileCaseSets = filterMolecularProfileCaseSets(molecularProfile, molecularProfileCaseSets);
Map<String, List<MolecularProfileCaseIdentifier>> filteredMolecularProfileCaseSets = filterMolecularProfileCaseSets(molecularProfile, molecularProfileCaseSets);

List<GenericAssayCategoricalEnrichment> genericAssayCategoricalEnrichments = expressionEnrichmentUtil.getGenericAssayCategoricalEnrichments(molecularProfile,
filteredMolecularProfileCaseSets, enrichmentType, maItr);
Expand All @@ -216,30 +203,24 @@ public List<GenericAssayCategoricalEnrichment> getGenericAssayCategoricalEnrichm
return enrichmentDatum;
}).collect(Collectors.toList());
}

private MolecularProfile getAndValidateMolecularProfile(String molecularProfileId, boolean isBinary) throws MolecularProfileNotFoundException {
private MolecularProfile getAndValidateMolecularProfile(String molecularProfileId, String dataType) throws MolecularProfileNotFoundException {
MolecularProfile molecularProfile = molecularProfileService.getMolecularProfile(molecularProfileId);
validateMolecularProfile(molecularProfile, Arrays.asList(MolecularProfile.MolecularAlterationType.GENERIC_ASSAY), isBinary);
validateMolecularProfile(molecularProfile, Arrays.asList(MolecularProfile.MolecularAlterationType.GENERIC_ASSAY), dataType);
return molecularProfile;
}

private void validateMolecularProfile(MolecularProfile molecularProfile,
List<MolecularProfile.MolecularAlterationType> validMolecularAlterationTypes,
boolean isBinary) throws MolecularProfileNotFoundException {
String dataType) throws MolecularProfileNotFoundException {
if (!validMolecularAlterationTypes.contains(molecularProfile.getMolecularAlterationType())) {
// Check alteration type
throw new MolecularProfileNotFoundException(molecularProfile.getStableId());
}
// Check datatype for binary or categorical
if(isBinary) {
if(!molecularProfile.getDatatype().equals("BINARY")) {
throw new MolecularProfileNotFoundException(molecularProfile.getStableId());
}
} else {
if(!molecularProfile.getDatatype().equals("CATEGORICAL")) {
throw new MolecularProfileNotFoundException(molecularProfile.getStableId());
}
}
if(molecularProfile.getMolecularAlterationType().equals(MolecularProfile.MolecularAlterationType.GENERIC_ASSAY) &&
!molecularProfile.getDatatype().equals(dataType))
throw new MolecularProfileNotFoundException(molecularProfile.getStableId());
}

private Map<String, List<MolecularProfileCaseIdentifier>> filterMolecularProfileCaseSets(MolecularProfile molecularProfile, Map<String, List<MolecularProfileCaseIdentifier>> molecularProfileCaseSets) {
Expand Down
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