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SCRUM-5952 enable transgenic constructs to be displayed. #1564

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Merged
cmpich merged 2 commits into from
Apr 10, 2026
Merged

SCRUM-5952 enable transgenic constructs to be displayed. #1564

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a113606
SCRUM-5952 enable transgenic constructs to be displayed.
cmpich Apr 10, 2026
b052815
Merge branch 'stage' into SCRUM-5952
cmpich Apr 10, 2026
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6 changes: 3 additions & 3 deletions agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java
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Expand Up @@ -19,7 +19,7 @@
import org.alliancegenome.core.exceptions.RestErrorMessage;
import org.alliancegenome.core.translators.tdf.AlleleToTdfTranslator;
import org.alliancegenome.curation_api.model.document.es.AlleleSummaryDocument;
import org.alliancegenome.curation_api.model.document.es.TransgenicAlleleDocument;
import org.alliancegenome.api.entity.TransgenicAlleleSummaryDocument;
import org.alliancegenome.curation_api.model.document.es.VariantSummaryDocument;
import org.alliancegenome.es.model.query.FieldFilter;
import org.alliancegenome.es.model.query.Pagination;
Expand Down Expand Up @@ -67,8 +67,8 @@ public AlleleSummaryDocument getAllele(String id) {
}

@Override
public TransgenicAlleleDocument getAlleleConstructs(String alleleId) {
JsonResultResponse<TransgenicAlleleDocument> transgenicAlleles = alleleEsService.getTransgenicAlleles(alleleId);
public TransgenicAlleleSummaryDocument getAlleleConstructs(String alleleId) {
JsonResultResponse<TransgenicAlleleSummaryDocument> transgenicAlleles = alleleEsService.getTransgenicAlleles(alleleId);
if (transgenicAlleles == null) {
return null;
}
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4 changes: 2 additions & 2 deletions agr_api/src/main/java/org/alliancegenome/api/rest/interfaces/AlleleRESTInterface.java
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Expand Up @@ -4,7 +4,7 @@
import org.alliancegenome.api.entity.AllelePhenotypeAnnotationDocument;
import org.alliancegenome.cache.repository.helper.JsonResultResponse;
import org.alliancegenome.curation_api.model.document.es.AlleleSummaryDocument;
import org.alliancegenome.curation_api.model.document.es.TransgenicAlleleDocument;
import org.alliancegenome.api.entity.TransgenicAlleleSummaryDocument;
import org.alliancegenome.curation_api.model.document.es.VariantSummaryDocument;
import org.alliancegenome.neo4j.view.PublicView;
import org.apache.commons.lang3.ObjectUtils.Null;
Expand Down Expand Up @@ -48,7 +48,7 @@ public interface AlleleRESTInterface {
@Operation(description = "Searches for transgenic alleles", summary = "Transgenic Alleles")
@APIResponses(value = {@APIResponse(responseCode = "404", description = "Missing transgenic alleles", content = @Content(mediaType = "text/plain")),
@APIResponse(responseCode = "200", description = "Search for alleles.", content = @Content(mediaType = "application/json", schema = @Schema(implementation = Null.class)))})
TransgenicAlleleDocument getAlleleConstructs(@Parameter(in = ParameterIn.PATH, name = "id", description = "Search for constructs for a given Allele by ID", required = true, schema = @Schema(type = SchemaType.STRING)) @PathParam("id") String id);
TransgenicAlleleSummaryDocument getAlleleConstructs(@Parameter(in = ParameterIn.PATH, name = "id", description = "Search for constructs for a given Allele by ID", required = true, schema = @Schema(type = SchemaType.STRING)) @PathParam("id") String id);

@GET
@Path("/{id}/variants")
Expand Down
12 changes: 6 additions & 6 deletions agr_api/src/main/java/org/alliancegenome/api/service/AlleleESService.java
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Expand Up @@ -13,7 +13,7 @@
import org.alliancegenome.cache.repository.helper.JsonResultResponse;
import org.alliancegenome.curation_api.model.document.es.AlleleSummaryDocument;
import org.alliancegenome.curation_api.model.document.es.ESDocument;
import org.alliancegenome.curation_api.model.document.es.TransgenicAlleleDocument;
import org.alliancegenome.api.entity.TransgenicAlleleSummaryDocument;
import org.alliancegenome.curation_api.model.document.es.VariantSummaryDocument;
import org.alliancegenome.es.model.query.Pagination;
import org.elasticsearch.action.search.SearchResponse;
Expand Down Expand Up @@ -64,23 +64,23 @@ public class AlleleESService extends ESService {
put(null, defaultSortMap);
}};

public JsonResultResponse<TransgenicAlleleDocument> getTransgenicAlleles(String alleleId) {
public JsonResultResponse<TransgenicAlleleSummaryDocument> getTransgenicAlleles(String alleleId) {
BoolQueryBuilder bool = boolQuery();
BoolQueryBuilder bool2 = boolQuery();
bool.must(bool2);
// ToDo: Change this class such that the category is public
// TransgenicAlleleDocument.category
// TransgenicAlleleSummaryDocument.category
bool.filter(new TermQueryBuilder("category", "transgenic_allele_summary"));
bool2.should(new MatchQueryBuilder("allele.primaryExternalId.keyword", alleleId));

JsonResultResponse<TransgenicAlleleDocument> ret = new JsonResultResponse<>();
JsonResultResponse<TransgenicAlleleSummaryDocument> ret = new JsonResultResponse<>();

SearchResponse searchResponse = getSearchResponse(bool, new Pagination(), null, false);
ret.setTotal((int) searchResponse.getHits().getTotalHits().value);
List<TransgenicAlleleDocument> list = new ArrayList<>();
List<TransgenicAlleleSummaryDocument> list = new ArrayList<>();
Arrays.stream(searchResponse.getHits().getHits()).forEach(searchHit -> {
try {
TransgenicAlleleDocument object = mapper.readValue(searchHit.getSourceAsString(), TransgenicAlleleDocument.class);
TransgenicAlleleSummaryDocument object = mapper.readValue(searchHit.getSourceAsString(), TransgenicAlleleSummaryDocument.class);
list.add(object);
} catch (Exception e) {
e.printStackTrace();
Expand Down
9 changes: 9 additions & 0 deletions ...ore/src/main/java/org/alliancegenome/core/variant/converters/VariantSummaryConverter.java
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Expand Up @@ -262,6 +262,15 @@ public List<VariantSummaryDocument> convertContextToDocument(VariantContext ctx,
allele.setTaxon(taxon);
// If we want to show

// Sort PVCs by most severe consequence
consequences.sort(Comparator.comparingInt(pvc -> {
if (pvc.getVepConsequences() == null || pvc.getVepConsequences().isEmpty()) {
return Integer.MAX_VALUE;
}
return pvc.getVepConsequences().stream()
.mapToInt(c -> c.getSeverityOrder() != null ? c.getSeverityOrder() : Integer.MAX_VALUE)
.min().orElse(Integer.MAX_VALUE);
}));
cvgla.setPredictedVariantConsequences(consequences);
// Create the document for each consequence (full flattening)
VariantSummaryDocument doc = new VariantSummaryDocument();
Expand Down
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