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SCRUM-3999 make gene-page phenotype table filterable by data provider #1256

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Merged
oblodgett merged 1 commit into from
Mar 6, 2025
Merged

SCRUM-3999 make gene-page phenotype table filterable by data provider #1256

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4 changes: 4 additions & 0 deletions agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -463,11 +463,13 @@ public JsonResultResponse<GenePhenotypeAnnotationDocument> getPhenotypeAnnotatio
String geneticEntityType,
String phenotype,
String reference,
String dataProvider,
String asc) {
long startTime = System.currentTimeMillis();
Pagination pagination = new Pagination(page, limit, sortBy, asc);
pagination.addFilterOption("phenotypeStatement", phenotype);
pagination.addFilterOption("pubmedPubModIDs", reference);
pagination.addFilterOption("primaryAnnotations.dataProvider.abbreviation", dataProvider);
try {
JsonResultResponse<GenePhenotypeAnnotationDocument> phenotypes = phenotypeESService.getGenePhenotypeAnnotations(id, pagination, false);
phenotypes.setHttpServletRequest(null);
Expand All @@ -489,6 +491,7 @@ public Response getPhenotypeAnnotationsDownloadFile(
String geneticEntityType,
String phenotype,
String reference,
String dataProvider,
String asc) {
// retrieve all records
JsonResultResponse<GenePhenotypeAnnotationDocument> response =
Expand All @@ -497,6 +500,7 @@ public Response getPhenotypeAnnotationsDownloadFile(
geneticEntityType,
phenotype,
reference,
dataProvider,
asc);
Response.ResponseBuilder responseBuilder = Response.ok(translator.getAllRows(response.getResults()));
APIServiceHelper.setDownloadHeader(id, EntityType.GENE, EntityType.PHENOTYPE, responseBuilder);
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2 changes: 2 additions & 0 deletions agr_api/src/main/java/org/alliancegenome/api/rest/interfaces/GeneRESTInterface.java
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Expand Up @@ -274,6 +274,7 @@ JsonResultResponse<GenePhenotypeAnnotationDocument> getPhenotypeAnnotations(
@QueryParam("filter.termName") String phenotype,
@Parameter(in = ParameterIn.QUERY, name = "filter.reference", description = "Reference number: PUBMED or a Pub ID from the MOD", schema = @Schema(type = SchemaType.STRING))
@QueryParam("filter.reference") String reference,
@Parameter(in = ParameterIn.QUERY, name = "filter.dataProvider", description = "Source", schema = @Schema(type = SchemaType.STRING)) @QueryParam("filter.dataProvider") String filterSource,
@Parameter(in = ParameterIn.QUERY, name = "asc", description = "order to sort by", schema = @Schema(type = SchemaType.STRING))
@DefaultValue("true") @QueryParam("asc") String asc);

Expand All @@ -296,6 +297,7 @@ Response getPhenotypeAnnotationsDownloadFile(
@QueryParam("filter.termName") String phenotype,
@Parameter(in = ParameterIn.QUERY, name = "filter.reference", description = "Reference number: PUBMED or a Pub ID from the MOD", schema = @Schema(type = SchemaType.STRING))
@QueryParam("filter.reference") String reference,
@Parameter(in = ParameterIn.QUERY, name = "filter.dataProvider", description = "Source", schema = @Schema(type = SchemaType.STRING)) @QueryParam("filter.dataProvider") String filterSource,
@Parameter(in = ParameterIn.QUERY, name = "asc", description = "order to sort by", schema = @Schema(type = SchemaType.STRING))
@DefaultValue("true")
@QueryParam("asc") String asc);
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