Skip to content

SCRUM-2758 Use taxon.species.fullName for species filtering #1545

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
oblodgett merged 3 commits into from
Apr 1, 2026
Merged

SCRUM-2758 Use taxon.species.fullName for species filtering #1545

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
3fb3859
SCRUM-2758 Use taxon.species.fullName for species filtering
oblodgett Apr 1, 2026
884dfd9
SCRUM-2758 Remove duplicate species filter in DiseaseController
oblodgett Apr 1, 2026
529b025
SCRUM-2758 Bump curation version to v0.47.24
oblodgett Apr 1, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 4 additions & 12 deletions agr_api/src/main/java/org/alliancegenome/api/controller/DiseaseController.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -85,9 +85,8 @@ public JsonResultResponse<AlleleDiseaseAnnotationDocument> getDiseaseAnnotations
sortBy = SortingField.DISEASE_ALLELE_DEFAULT.toString();
}
Pagination pagination = new Pagination(page, limit, sortBy, asc);
pagination.addFilterOption("subject.taxon.name.keyword", species);
pagination.addFilterOption("subject.taxon.species.fullName.keyword", species);
pagination.addFilterOption("subject.alleleSymbol.displayText", alleleName);
pagination.addFilterOption("subject.taxon.name.keyword", species);
pagination.addFilterOption("evidenceCodes.abbreviation", evidenceCode);
pagination.addFilterOption("generatedRelationString.keyword", associationType);
pagination.addFilterOption("diseaseQualifiers.keyword", diseaseQualifier);
Expand Down Expand Up @@ -256,7 +255,7 @@ public JsonResultResponse<GeneDiseaseAnnotationDocument> getDiseaseAnnotationsBy
pagination.addFilterOption("subject.curie", geneID);
}
if (species != null) {
pagination.addFilterOption("subject.taxon.species.name.keyword", species);
pagination.addFilterOption("subject.taxon.species.fullName.keyword", species);
}


Expand Down Expand Up @@ -300,7 +299,7 @@ public JsonResultResponse<AGMDiseaseAnnotationDocument> getDiseaseAnnotationsFor
long startTime = System.currentTimeMillis();
Pagination pagination = new Pagination(page, limit, sortBy, asc);
pagination.addFilterOption("subject.agmFullName.displayText", modelName);
pagination.addFilterOption("subject.taxon.name.keyword", species);
pagination.addFilterOption("subject.taxon.species.fullName.keyword", species);
pagination.addFilterOption("evidenceCodes.abbreviation", evidenceCode);
pagination.addFilterOption("generatedRelationString.keyword", associationType);
pagination.addFilterOption("conditionModifierAggregated", conditionModifier);
Expand Down Expand Up @@ -414,14 +413,7 @@ private JsonResultResponse<GeneDiseaseAnnotationDocument> getDiseaseAnnotationsR
pagination.addFilterOption("primaryAnnotations.with.geneSymbol.displayText", basedOnGeneSymbol);
pagination.addFilterOption("primaryAnnotations.dataProvider.abbreviation OR primaryAnnotations.secondaryDataProvider.abbreviation", filterSource);

// TODO: remove when SC data is fixed:
if (filterSpecies != null) {
if (filterSpecies.equals("Saccharomyces cerevisiae")) {
pagination.addFilterOption("subject.taxon.name.keyword", "Saccharomyces cerevisiae S288C");
} else {
pagination.addFilterOption("subject.taxon.name.keyword", filterSpecies);
}
}
pagination.addFilterOption("subject.taxon.species.fullName.keyword", filterSpecies);

if (pagination.hasErrors()) {
RestErrorMessage message = new RestErrorMessage();
Expand Down
2 changes: 1 addition & 1 deletion agr_api/src/main/java/org/alliancegenome/api/controller/ExpressionController.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@ public JsonResultResponse<GeneExpressionDocument> getExpressionAnnotations(
private JsonResultResponse<GeneExpressionDocument> getExpressionDetailJsonResultResponse(List<String> geneIDs, String termID, String focusTaxonId, String filterSpecies, String filterGene, String filterStage, String filterAssay, String filterReference, String filterLocation, String filterSource, Integer limit, Integer page, String sortBy, String asc) {
long startTime = System.currentTimeMillis();
Pagination pagination = new Pagination(page, limit, sortBy, asc);
pagination.addFilterOption("geneExpressionAnnotation.expressionAnnotationSubject.taxon.name", filterSpecies);
pagination.addFilterOption("geneExpressionAnnotation.expressionAnnotationSubject.taxon.species.fullName.keyword", filterSpecies);
pagination.addFilterOption("geneExpressionAnnotation.expressionAnnotationSubject.geneSymbol.displayText", filterGene);
pagination.addFilterOption("geneExpressionAnnotation.whereExpressedStatement", filterLocation);
pagination.addFilterOption("geneExpressionAnnotation.whenExpressedStageName", filterStage);
Expand Down
34 changes: 5 additions & 29 deletions agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -226,13 +226,7 @@ public JsonResultResponse<GeneGeneticInteractionDocument> getGeneticInteractions
pagination.addFilterOption("geneGeneticInteraction.interactorBGeneticPerturbation.alleleSymbol.displayText", interactorGeneticPerturbation);
pagination.addFilterOption("geneGeneticInteraction.phenotypesOrTraits", phenotypes);
pagination.addFilterOption("geneGeneticInteraction.interactionType.name.keyword", interactionType);
if (interactorSpecies != null) {
if (interactorSpecies.equals("Saccharomyces cerevisiae")) {
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.taxon.name.keyword", "Saccharomyces cerevisiae S288C");
} else {
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.taxon.name.keyword", interactorSpecies);
}
}
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.taxon.species.fullName.keyword", interactorSpecies);
// Todo: needs to be made generic
// pagination.validateFilterValues(info.getQueryParameters());
if (pagination.hasErrors()) {
Expand Down Expand Up @@ -269,13 +263,7 @@ public Response getGeneticInteractionsDownload(String id, String sortBy, String
pagination.addFilterOption("geneGeneticInteraction.interactorBGeneticPerturbation.alleleSymbol.displayText", interactorGeneticPerturbation);
pagination.addFilterOption("geneGeneticInteraction.phenotypesOrTraits", phenotypes);
pagination.addFilterOption("geneGeneticInteraction.interactionType.name.keyword", interactionType);
if (interactorSpecies != null) {
if (interactorSpecies.equals("Saccharomyces cerevisiae")) {
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.taxon.name.keyword", "Saccharomyces cerevisiae S288C");
} else {
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.taxon.name.keyword", interactorSpecies);
}
}
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.taxon.species.fullName.keyword", interactorSpecies);

JsonResultResponse<GeneGeneticInteractionDocument> interactions = geneService.getGeneticInteractions(id, pagination);

Expand All @@ -298,13 +286,7 @@ public JsonResultResponse<GeneMolecularInteractionDocument> getMolecularInteract
pagination.addFilterOption("geneMolecularInteraction.evidence.referenceID", reference);
pagination.addFilterOption("geneMolecularInteraction.interactorBType.name.keyword", interactorMoleculeType);
pagination.addFilterOption("geneMolecularInteraction.detectionMethod.name.keyword", detectionMethod);
if (interactorSpecies != null) {
if (interactorSpecies.equals("Saccharomyces cerevisiae")) {
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.taxon.name.keyword", "Saccharomyces cerevisiae S288C");
} else {
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.taxon.name.keyword", interactorSpecies);
}
}
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.taxon.species.fullName.keyword", interactorSpecies);
// Todo: needs to be made generic
// pagination.validateFilterValues(info.getQueryParameters());
if (pagination.hasErrors()) {
Expand Down Expand Up @@ -337,13 +319,7 @@ public Response getMolecularInteractionsDownload(String id, String sortBy, Strin
pagination.addFilterOption("geneMolecularInteraction.evidence.referenceID", reference);
pagination.addFilterOption("geneMolecularInteraction.interactorBType.name.keyword", interactorMoleculeType);
pagination.addFilterOption("geneMolecularInteraction.detectionMethod.name.keyword", detectionMethod);
if (interactorSpecies != null) {
if (interactorSpecies.equals("Saccharomyces cerevisiae")) {
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.taxon.name.keyword", "Saccharomyces cerevisiae S288C");
} else {
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.taxon.name.keyword", interactorSpecies);
}
}
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.taxon.species.fullName.keyword", interactorSpecies);
JsonResultResponse<GeneMolecularInteractionDocument> interactions = geneService.getMolecularInteractions(id, pagination);

Response.ResponseBuilder responseBuilder = Response.ok(molecularInteractionTranslator.getAllRows(interactions.getResults()));
Expand Down Expand Up @@ -482,7 +458,7 @@ public JsonResultResponse<GeneTransgenicAlleleSummaryDocument> getTransgenicAlle
sortBy = "transgenicAllele";
}
Pagination pagination = new Pagination(page, limit, sortBy, null);
pagination.addFilterOption("alleleDocument.allele.taxon.name", species);
pagination.addFilterOption("alleleDocument.allele.taxon.species.fullName.keyword", species);
pagination.addFilterOption("alleleDocument.allele.alleleSymbol.formatText", alleleSymbol);
pagination.addFilterOption("alleleDocument.transgenicAlleleConstructs.construct.constructSymbol.formatText", constructSymbol);
pagination.addFilterOption("alleleDocument.transgenicAlleleConstructs.regulatoryGenes.geneSymbol.formatText", constructRegulatedGene);
Expand Down
8 changes: 4 additions & 4 deletions agr_api/src/main/java/org/alliancegenome/api/service/DiseaseESService.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -109,7 +109,7 @@ private Map<String, Object> getSupplementalData(String focusTaxonId, boolean use
// create histogram of select columns of unfiltered query
Map<String, String> aggregationFields = new HashMap<>();
if (useSpeciesAggregation) {
aggregationFields.put("subject.taxon.name.keyword", "species");
aggregationFields.put("subject.taxon.species.fullName.keyword", "species");
}
aggregationFields.put("generatedRelationString.keyword", "associationType");
aggregationFields.put("diseaseQualifiers.keyword", "diseaseQualifiers");
Expand Down Expand Up @@ -277,7 +277,7 @@ public JsonResultResponse<GeneDiseaseAnnotationDocument> getDiseaseAnnotationsWi
sortingSetMap.put("default", List.of("viaOrthologyOrder", "phylogeneticSortingIndex", "subject.geneSymbol.displayText.sort"));
sortingSetMap.put("gene", List.of("subject.geneSymbol.displayText.sort", "phylogeneticSortingIndex"));
sortingSetMap.put("disease", List.of("object.name.sort", "phylogeneticSortingIndex", "subject.geneSymbol.displayText.sort"));
sortingSetMap.put("species", List.of("subject.taxon.name.keyword", "subject.geneSymbol.displayText.sort"));
sortingSetMap.put("species", List.of("subject.taxon.species.fullName.keyword", "subject.geneSymbol.displayText.sort"));

LinkedHashMap<String, SortOrder> sortingMap = new LinkedHashMap<>();

Expand Down Expand Up @@ -324,7 +324,7 @@ public JsonResultResponse<AGMDiseaseAnnotationDocument> getDiseaseAnnotationsWit
sortingSetMap.put("default", List.of("phylogeneticSortingIndex", "subject.name.sort"));
sortingSetMap.put("model", List.of("subject.name.sort", "phylogeneticSortingIndex"));
sortingSetMap.put("disease", List.of("object.name.sort", "phylogeneticSortingIndex", "subject.name.sort"));
sortingSetMap.put("species", List.of("subject.taxon.name.keyword", "subject.name.sort"));
sortingSetMap.put("species", List.of("subject.taxon.species.fullName.keyword", "subject.name.sort"));

LinkedHashMap<String, SortOrder> sortingMap = new LinkedHashMap<>();

Expand Down Expand Up @@ -372,7 +372,7 @@ public JsonResultResponse<AlleleDiseaseAnnotationDocument> getDiseaseAnnotations
sortingSetMap.put("default", List.of("phylogeneticSortingIndex", "subject.alleleSymbol.displayText.sort"));
sortingSetMap.put("allele", List.of("subject.alleleSymbol.displayText.sort", "phylogeneticSortingIndex"));
sortingSetMap.put("disease", List.of("object.name.sort", "phylogeneticSortingIndex", "subject.alleleSymbol.displayText.sort"));
sortingSetMap.put("species", List.of("subject.taxon.name.keyword", "subject.alleleSymbol.displayText.sort"));
sortingSetMap.put("species", List.of("subject.taxon.species.fullName.keyword", "subject.alleleSymbol.displayText.sort"));

LinkedHashMap<String, SortOrder> sortingMap = new LinkedHashMap<>();

Expand Down
4 changes: 2 additions & 2 deletions agr_api/src/main/java/org/alliancegenome/api/service/ExpressionESService.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@ private LinkedHashMap<String, SortOrder> getExpressionSortOrders(Pagination pagi
LinkedHashMap<String, SortOrder> sortingMap = new LinkedHashMap<>();
LinkedHashMap<String, String> sortingSetMap = new LinkedHashMap<>();

sortingSetMap.put("species", "geneExpressionAnnotation.expressionAnnotationSubject.taxon.name.keyword");
sortingSetMap.put("species", "geneExpressionAnnotation.expressionAnnotationSubject.taxon.species.fullName.keyword");
sortingSetMap.put("gene", "geneExpressionAnnotation.expressionAnnotationSubject.geneSymbol.displayText.sort");
sortingSetMap.put("location", "geneExpressionAnnotation.whereExpressedStatement.sort");
sortingSetMap.put("stage", "geneExpressionAnnotation.whenExpressedStageName.sort");
Expand Down Expand Up @@ -131,7 +131,7 @@ private LinkedHashMap<String, SortOrder> getExpressionSortOrders(Pagination pagi
private Map<String, Object> getSupplementalData(BoolQueryBuilder unfilteredQuery) {

Map<String, String> aggregationFields = new HashMap<>();
aggregationFields.put("geneExpressionAnnotation.expressionAnnotationSubject.taxon.name.keyword", "species");
aggregationFields.put("geneExpressionAnnotation.expressionAnnotationSubject.taxon.species.fullName.keyword", "species");
aggregationFields.put("geneExpressionAnnotation.whereExpressedStatement.keyword", "location");
aggregationFields.put("geneExpressionAnnotation.whenExpressedStageName.keyword", "stage");
aggregationFields.put("geneExpressionAnnotation.expressionAssayUsed.name.keyword", "assay");
Expand Down
4 changes: 2 additions & 2 deletions agr_api/src/main/java/org/alliancegenome/api/service/GeneService.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -156,7 +156,7 @@ private Map<String, Object> getGeneticInteractionSupplementalData(BoolQueryBuild
aggregationFields.put("geneGeneticInteraction.interactorARole.name.keyword", "filter.role");
aggregationFields.put("geneGeneticInteraction.interactorBRole.name.keyword", "filter.interactorRole");
aggregationFields.put("geneGeneticInteraction.interactionType.name.keyword", "filter.interactionType");
aggregationFields.put("geneGeneticInteraction.geneGeneAssociationObject.taxon.name.keyword", "filter.interactorSpecies");
aggregationFields.put("geneGeneticInteraction.geneGeneAssociationObject.taxon.species.fullName.keyword", "filter.interactorSpecies");
return getInteractionSupplementalData(aggregationFields, unfilteredQuery);
}

Expand All @@ -165,7 +165,7 @@ private Map<String, Object> getMolecularInteractionSupplementalData(BoolQueryBui
aggregationFields.put("geneMolecularInteraction.interactorBType.name.keyword", "filter.interactorMoleculeType");
aggregationFields.put("geneMolecularInteraction.interactorAType.name.keyword", "filter.moleculeType");
aggregationFields.put("geneMolecularInteraction.detectionMethod.name.keyword", "filter.detectionMethod");
aggregationFields.put("geneMolecularInteraction.geneGeneAssociationObject.taxon.name.keyword", "filter.interactorSpecies");
aggregationFields.put("geneMolecularInteraction.geneGeneAssociationObject.taxon.species.fullName.keyword", "filter.interactorSpecies");
return getInteractionSupplementalData(aggregationFields, unfilteredQuery);
}

Expand Down
2 changes: 1 addition & 1 deletion agr_api/src/main/java/org/alliancegenome/api/service/TransgenicAlleleESService.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ public JsonResultResponse<GeneTransgenicAlleleSummaryDocument> getTransgenicAlle
BoolQueryBuilder query = getBaseModelQuery(List.of(geneId), false, "transgenic_allele_annotations");

JsonResultResponse<GeneTransgenicAlleleSummaryDocument> ret = new JsonResultResponse<>();
Map<String, String> aggregationFields = Map.of("alleleDocument.allele.taxon.name.keyword", "species");
Map<String, String> aggregationFields = Map.of("alleleDocument.allele.taxon.species.fullName.keyword", "species");
ret.setSupplementalData(getSupplementalData(geneId, true, debug, query, aggregationFields));

// add table filter
Expand Down
5 changes: 5 additions & 0 deletions agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -137,6 +137,7 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
new FieldBuilder(builder, "object.name", "text").keyword().sort().build(); // gene_disease_annotation, allele_disease_annotation, agm_disease_annotation
new FieldBuilder(builder, "object.curie", "text").keyword().sort().build(); // gene_disease_annotation, allele_disease_annotation, agm_disease_annotation
new FieldBuilder(builder, "subject.primaryExternalId", "text").keyword().sort().build(); // gene_disease_annotation, allele_disease_annotation, agm_disease_annotation
new FieldBuilder(builder, "subject.taxon.species.fullName", "text").keyword().sort().build(); // gene_disease_annotation, allele_disease_annotation, agm_disease_annotation

new FieldBuilder(builder, "anatomicalExpressionSlim", "text").keyword().build(); // gene, dataset
new FieldBuilder(builder, "whereExpressed", "text").keyword().build(); // gene, dataset
Expand All @@ -148,6 +149,7 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
new FieldBuilder(builder, "model.agmFullName.displayText", "text").keyword().sort().build(); //
new FieldBuilder(builder, "model.agmFullName.formatText", "text").keyword().sort().build(); //
new FieldBuilder(builder, "alleleDocument.allele.alleleSymbol.formatText", "text").keyword().sort().build(); //
new FieldBuilder(builder, "alleleDocument.allele.taxon.species.fullName", "text").keyword().sort().build(); //
new FieldBuilder(builder, "alleleDocument.phylogeneticSortingIndex", "long").keyword().sort().build(); //
new FieldBuilder(builder, "definition", "text").standardText().build(); // go, disease

Expand Down Expand Up @@ -193,6 +195,7 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
builder.endObject();
new FieldBuilder(builder, "geneMolecularInteraction.geneGeneAssociationObject.geneSymbol.displayText", "text").keyword().sort().build();
new FieldBuilder(builder, "geneMolecularInteraction.geneGeneAssociationObject.taxon.name", "text").keyword().sort().build();
new FieldBuilder(builder, "geneMolecularInteraction.geneGeneAssociationObject.taxon.species.fullName", "text").keyword().sort().build();
new FieldBuilder(builder, "geneMolecularInteraction.geneAssociationSubject.curie", "text").keyword().build();
new FieldBuilder(builder, "geneMolecularInteraction.geneAssociationSubject.primaryExternalId", "text").keyword().build();
new FieldBuilder(builder, "geneMolecularInteraction.interactorAType.name", "text").keyword().sort().build();
Expand All @@ -211,6 +214,7 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
builder.endObject();
new FieldBuilder(builder, "geneGeneticInteraction.geneGeneAssociationObject.geneSymbol.displayText", "text").keyword().sort().build();
new FieldBuilder(builder, "geneGeneticInteraction.geneGeneAssociationObject.taxon.name", "text").keyword().sort().build();
new FieldBuilder(builder, "geneGeneticInteraction.geneGeneAssociationObject.taxon.species.fullName", "text").keyword().sort().build();
new FieldBuilder(builder, "geneGeneticInteraction.geneAssociationSubject.curie", "text").keyword().build();
new FieldBuilder(builder, "geneGeneticInteraction.geneAssociationSubject.primaryExternalId", "text").keyword().build();
new FieldBuilder(builder, "geneGeneticInteraction.interactorARole.name", "text").keyword().build();
Expand Down Expand Up @@ -255,6 +259,7 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
new FieldBuilder(builder, "geneExpressionAnnotation.expressionAnnotationSubject.geneSymbol.displayText", "text").keyword().sort().build();
new FieldBuilder(builder, "geneExpressionAnnotation.expressionAnnotationSubject.primaryExternalId", "text").keyword().build();
new FieldBuilder(builder, "geneExpressionAnnotation.expressionAnnotationSubject.taxon.name", "text").keyword().sort().build();
new FieldBuilder(builder, "geneExpressionAnnotation.expressionAnnotationSubject.taxon.species.fullName", "text").keyword().sort().build();
new FieldBuilder(builder, "geneExpressionAnnotation.whereExpressedStatement", "text").keyword().sort().build();
new FieldBuilder(builder, "geneExpressionAnnotation.whenExpressedStageName", "text").keyword().sort().build();
new FieldBuilder(builder, "geneExpressionAnnotation.expressionAssayUsed.name", "text").keyword().sort().build();
Expand Down
2 changes: 1 addition & 1 deletion pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
<maven-checkstyle-plugin.version>3.3.1</maven-checkstyle-plugin.version>
<checkstyle.version>10.17.0</checkstyle.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<curation.version>v0.47.21</curation.version>
<curation.version>v0.47.24</curation.version>
</properties>
<dependencyManagement>
<dependencies>
Expand Down
Loading