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Partial updates
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@calvinlu3
calvinlu3 committed Feb 8, 2024
1 parent 97926c7 commit 90a421a
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Showing 3 changed files with 314 additions and 354 deletions.
2 changes: 1 addition & 1 deletion core/src/main/java/org/mskcc/cbio/oncokb/util/IndicatorUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -379,7 +379,7 @@ public static IndicatorQueryResp processQuery(Query query,
}

// Mutation summary
if (evidenceTypes.contains(EvidenceType.MUTATION_SUMMARY)) {
if (evidenceTypes.contains(EvidenceType.MUTATION_SUMMARY) && StringUtils.isNotEmpty(matchedAlt.getAlteration())) {
indicatorQuery.setVariantSummary(SummaryUtils.variantSummary(gene, matchedAlt,
new ArrayList<>(relevantAlterations), query));
}
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313 changes: 313 additions & 0 deletions web/src/main/java/org/mskcc/cbio/oncokb/api/pub/v1/AnnotationsApiController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
import org.springframework.web.bind.annotation.RequestParam;

import java.util.*;
import java.util.stream.Collectors;

/**
* Created by Hongxin Zhang on 2019-03-25.
Expand Down Expand Up @@ -517,6 +518,182 @@ public ResponseEntity<List<IndicatorQueryResp>> annotateStructuralVariantsPost(
return new ResponseEntity<>(result, status);
}

@PremiumPublicApi
@ApiOperation(value = "", notes = "Get annotations based on search", response = AnnotationSearchResult.class, responseContainer = "List")
@ApiResponses(value = {
@ApiResponse(code = 200, message = "OK")})
@RequestMapping(value = "/annotation/search",
produces = {"application/json"},
method = RequestMethod.GET)
ResponseEntity<LinkedHashSet<AnnotationSearchResult>> annotationSearchGet(
@ApiParam(value = "The search query, it could be hugoSymbol, variant or cancer type. At least two characters. Maximum two keywords are supported, separated by space", required = true) @RequestParam(value = "query") String query,
@ApiParam(value = "The limit of returned result.") @RequestParam(value = "limit", defaultValue = "10", required = false) Integer limit
) {
final int DEFAULT_LIMIT = 10;
final int QUERY_MIN_LENGTH = 2;
TreeSet<AnnotationSearchResult> result = new TreeSet<>(new AnnotationSearchResultComp(query));
if(limit == null) {
limit = DEFAULT_LIMIT;
}
if (query != null && query.length() >= QUERY_MIN_LENGTH) {
List<String> keywords = Arrays.asList(query.trim().split("\\s+"));

if (keywords.size() == 1) {
// Blur search gene
result.addAll(findActionableGenesByGeneSearch(keywords.get(0)));

// // Blur search variant
result.addAll(findActionableGenesByAlterationSearch(keywords.get(0)));

// // // Blur search cancer type
result.addAll(findActionalGenesByCancerType(keywords.get(0)));

// // If the keyword contains dash and result is empty, then we should return both fusion genes
if (keywords.get(0).contains("-") && result.isEmpty()) {
for (String subKeyword : keywords.get(0).split("-")) {
result.addAll(findActionableGenesByGeneSearch(subKeyword));
}
}
} else {
// Assume that the first keyword is a gene, followed by alteration
// Todo: We should be able to find the gene even if it is not the first keyword.
Set<Gene> geneMatches = new HashSet<>();
if (keywords.get(0).contains("-")) {
Set<Gene> subGenes = new HashSet<>();
for (String subKeyword : keywords.get(0).split("-")) {
subGenes.addAll(GeneUtils.searchGene(subKeyword, false));
}
geneMatches.addAll(subGenes);
} else {
geneMatches.addAll(GeneUtils.searchGene(keywords.get(0), false));
}

String alterationKeywords = StringUtils.join(keywords.subList(1, keywords.size()), " ");
List<Alteration> altMatches = AlterationUtils.lookupVariant(alterationKeywords, false, true, AlterationUtils.getAllAlterations())
.stream()
.filter(alt -> geneMatches.contains(alt.getGene()))
.collect(Collectors.toList());
for (Gene gene: geneMatches) {
for (Alteration alteration: altMatches) {
Query indicatorQuery = new Query();
indicatorQuery.setEntrezGeneId(gene.getEntrezGeneId());
indicatorQuery.setHugoSymbol(gene.getHugoSymbol());
indicatorQuery.setAlteration(alteration.getAlteration());
AnnotationSearchResult annotationSearchResult = new AnnotationSearchResult();
annotationSearchResult.setQueryType(AnnotationSearchQueryType.VARIANT);
annotationSearchResult.setIndicatorQueryResp(IndicatorUtils.processQuery(indicatorQuery, null, null, null));
if (annotationSearchResult.getIndicatorQueryResp().getVariantExist()) {
result.add(annotationSearchResult);
}
}
}

// // If there is no match, the keywords could referring to a variant, try to do a blur variant search
String fullKeywords = StringUtils.join(keywords, " ");
result.addAll(findActionableGenesByAlterationSearch(fullKeywords));

// // // Blur search for multi-word cancer type
result.addAll(findActionalGenesByCancerType(fullKeywords));
}
}

LinkedHashSet<AnnotationSearchResult> orderedResult = new LinkedHashSet<>();
orderedResult.addAll(result);

return new ResponseEntity<>(MainUtils.getLimit(orderedResult, limit), HttpStatus.OK);
}

private LinkedHashSet<AnnotationSearchResult> findActionableGenesByGeneSearch(String keyword) {
LinkedHashSet<AnnotationSearchResult> result = new LinkedHashSet<>();
Set<Gene> geneMatches = GeneUtils.searchGene(keyword, false);
for (Gene gene: geneMatches) {
Query query = new Query();
query.setEntrezGeneId(gene.getEntrezGeneId());
query.setHugoSymbol(gene.getHugoSymbol());
AnnotationSearchResult annotationSearchResult = new AnnotationSearchResult();
annotationSearchResult.setQueryType(AnnotationSearchQueryType.GENE);
annotationSearchResult.setIndicatorQueryResp(IndicatorUtils.processQuery(query, null, null, null));
result.add(annotationSearchResult);
}
return result;
}

private LinkedHashSet<AnnotationSearchResult> findActionableGenesByAlterationSearch(String keyword) {
LinkedHashSet<AnnotationSearchResult> result = new LinkedHashSet<>();
List<Alteration> altMatches = AlterationUtils.lookupVariant(keyword, false, true, AlterationUtils.getAllAlterations());
for (Alteration alteration: altMatches) {
Query indicatorQuery = new Query();
if (alteration.getName().toLowerCase().contains(keyword.toLowerCase())) {
indicatorQuery.setAlteration(alteration.getName());
} else {
indicatorQuery.setAlteration((alteration.getAlteration()));
}
indicatorQuery.setEntrezGeneId(alteration.getGene().getEntrezGeneId());
indicatorQuery.setHugoSymbol(alteration.getGene().getHugoSymbol());
AnnotationSearchResult annotationSearchResult = new AnnotationSearchResult();
annotationSearchResult.setQueryType(AnnotationSearchQueryType.VARIANT);
annotationSearchResult.setIndicatorQueryResp(IndicatorUtils.processQuery(indicatorQuery, null, null, null));
result.add(annotationSearchResult);
}
return result;
}

private LinkedHashSet<AnnotationSearchResult> findActionalGenesByCancerType(String query) {

Set<Evidence> allImplicationEvidences = EvidenceUtils.getEvidenceByEvidenceTypesAndLevels(EvidenceTypeUtils.getImplicationEvidenceTypes(), LevelUtils.getPublicLevels());

query = query.toLowerCase();

Set<TumorType> tumorTypeMatches = new HashSet<>();
for(Map.Entry<String, TumorType> subtype: CacheUtils.getLowercaseSubtypeTumorTypeMap().entrySet()) {
if(subtype.getKey().contains(query)) {
tumorTypeMatches.add(subtype.getValue());
}
}

for(Map.Entry<String, TumorType> mainType: CacheUtils.getMainTypeTumorTypeMap().entrySet()) {
if (mainType.getKey().toLowerCase().contains(query)) {
tumorTypeMatches.add(mainType.getValue());
}
}

if (tumorTypeMatches.isEmpty()) {
return new LinkedHashSet<>();
}

LinkedHashSet<AnnotationSearchResult> result = new LinkedHashSet<>();
Set<SearchObject> searchObjects = new HashSet<>();
for (TumorType tumorType : tumorTypeMatches) {
for (Evidence evidence : allImplicationEvidences) {
if (TumorTypeUtils.findEvidenceRelevantCancerTypes(evidence).contains(tumorType)) {
SearchObject searchObject = new SearchObject();
searchObject.setGene(evidence.getGene());
searchObject.setAlteration(evidence.getAlterations().iterator().next());
searchObject.setTumorType(tumorType);
searchObjects.add(searchObject);
}
}
}

for (SearchObject searchObject: searchObjects) {
Query indicatorQuery = new Query();
indicatorQuery.setEntrezGeneId(searchObject.getGene().getEntrezGeneId());
indicatorQuery.setHugoSymbol(searchObject.getGene().getHugoSymbol());
indicatorQuery.setAlteration(searchObject.getAlteration().getName());
if (searchObject.getTumorType().getMainType().toLowerCase().contains(query)) {
indicatorQuery.setTumorType(searchObject.getTumorType().getMainType());
} else {
indicatorQuery.setTumorType(searchObject.getTumorType().getSubtype());
}
AnnotationSearchResult annotationSearchResult = new AnnotationSearchResult();
annotationSearchResult.setQueryType(AnnotationSearchQueryType.CANCER_TYPE);
annotationSearchResult.setIndicatorQueryResp(IndicatorUtils.processQuery(indicatorQuery, null, null, null));
result.add(annotationSearchResult);
}

return result;
}



private IndicatorQueryResp getIndicatorQueryFromGenomicLocation(
Expand Down Expand Up @@ -600,3 +777,139 @@ private static Gene findGeneFromPool(Map<String, Gene> genePool, QueryGene query
return genePool.get(queryGene.getEntrezGeneId() == null ? queryGene.getHugoSymbol().toLowerCase() : queryGene.getEntrezGeneId().toString());
}
}

class AnnotationSearchResultComp implements Comparator<AnnotationSearchResult> {
private String keyword;

public AnnotationSearchResultComp(String keyword) {
this.keyword = keyword.toLowerCase();
}

@Override
public int compare(AnnotationSearchResult a1, AnnotationSearchResult a2) {
IndicatorQueryResp i1 = a1.getIndicatorQueryResp();
IndicatorQueryResp i2 = a2.getIndicatorQueryResp();

// Compare by query type
Integer result = MainUtils.compareAnnotationSearchQueryType(a1.getQueryType(), a2.getQueryType(), true);

String name1 = "";
String name2 = "";
if (result == 0) {
if (a1.getQueryType().equals(AnnotationSearchQueryType.GENE)) {
name1 = i1.getQuery().getHugoSymbol().toLowerCase();
name2 = i2.getQuery().getHugoSymbol().toLowerCase();
}
if (a1.getQueryType().equals(AnnotationSearchQueryType.VARIANT)) {
name1 = i1.getQuery().getAlteration().toLowerCase();
name2 = i2.getQuery().getAlteration().toLowerCase();
}
if (a1.getQueryType().equals(AnnotationSearchQueryType.CANCER_TYPE)) {
name1 = i1.getQuery().getTumorType().toLowerCase();
name2 = i2.getQuery().getTumorType().toLowerCase();
}
}
Integer index1 = name1.indexOf(this.keyword);
Integer index2 = name2.indexOf(this.keyword);
if (index1.equals(index2)) {
return compareLevel(i1, i2, name1, name2);
} else {
if (index1.equals(-1))
return 1;
if (index2.equals(-1))
return -1;
return compareLevel(i1, i2, name1, name2);
}

}

private Integer compareLevel(IndicatorQueryResp i1, IndicatorQueryResp i2, String name1, String name2) {
// Compare therapeutic levels
LevelOfEvidence i1Level = i1.getHighestSensitiveLevel();
LevelOfEvidence i2Level = i2.getHighestSensitiveLevel();
if (i1Level == null) {
i1Level = i1.getHighestResistanceLevel();
}
if (i2Level == null) {
i2Level = i2.getHighestResistanceLevel();
}
Integer result = LevelUtils.compareLevel(i1Level, i2Level, LevelUtils.getIndexedTherapeuticLevels());
if (result == 0) {
// Compare diagnostic level
result = LevelUtils.compareLevel(i1.getHighestDiagnosticImplicationLevel(), i2.getHighestDiagnosticImplicationLevel(), LevelUtils.getIndexedDiagnosticLevels());
if (result == 0) {
result = LevelUtils.compareLevel(i1.getHighestPrognosticImplicationLevel(), i2.getHighestPrognosticImplicationLevel(), LevelUtils.getIndexedPrognosticLevels());
if (result == 0) {
result = LevelUtils.compareLevel(i1.getHighestFdaLevel(), i2.getHighestFdaLevel(), LevelUtils.getIndexedFdaLevels());
if (result == 0) {
//Compare Oncogenicity. Treat YES, LIKELY as the same
Oncogenicity o1 = Oncogenicity.getByEffect(i1.getOncogenic());
Oncogenicity o2 = Oncogenicity.getByEffect(i2.getOncogenic());
if (o1 != null && o1.equals(Oncogenicity.LIKELY)) {
o1 = Oncogenicity.YES;
}
if (o2 != null && o2.equals(Oncogenicity.LIKELY)) {
o2 = Oncogenicity.YES;
}
result = MainUtils.compareOncogenicity(o1, o2, true);
if (result == 0) {
result = name1.compareTo(name2);
if (result == 0) {
result = i1.getQuery().getHugoSymbol().compareTo(i2.getQuery().getHugoSymbol());
}
}
}
return result;
}
}

}
return result;
}
}

class SearchObject {
private Gene gene;
private Alteration alteration;
private TumorType tumorType;

public Gene getGene() {
return this.gene;
}

public void setGene(Gene gene) {
this.gene = gene;
}

public Alteration getAlteration() {
return this.alteration;
}

public void setAlteration(Alteration alteration) {
this.alteration = alteration;
}

public TumorType getTumorType() {
return this.tumorType;
}

public void setTumorType(TumorType tumorType) {
this.tumorType = tumorType;
}

@Override
public boolean equals(Object o) {
if (this == o) return true;
if (!(o instanceof SearchObject)) return false;
SearchObject searchObject = (SearchObject) o;
return Objects.equals(getAlteration(), searchObject.getAlteration()) &&
Objects.equals(getGene(), searchObject.getGene()) &&
Objects.equals(getTumorType(), searchObject.getTumorType());
}

@Override
public int hashCode() {
return Objects.hash(getGene(), getAlteration(), getTumorType());
}

}
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