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Merge pull request #1545 from alliance-genome/SCRUM-2758
SCRUM-2758 Use taxon.species.fullName for species filtering
2 parents a28d606 + 529b025 commit 5618b26

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9 files changed

+25
-52
lines changed

9 files changed

+25
-52
lines changed

‎agr_api/src/main/java/org/alliancegenome/api/controller/DiseaseController.java‎

Lines changed: 4 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -85,9 +85,8 @@ public JsonResultResponse<AlleleDiseaseAnnotationDocument> getDiseaseAnnotations
8585
sortBy = SortingField.DISEASE_ALLELE_DEFAULT.toString();
8686
}
8787
Pagination pagination = new Pagination(page, limit, sortBy, asc);
88-
pagination.addFilterOption("subject.taxon.name.keyword", species);
88+
pagination.addFilterOption("subject.taxon.species.fullName.keyword", species);
8989
pagination.addFilterOption("subject.alleleSymbol.displayText", alleleName);
90-
pagination.addFilterOption("subject.taxon.name.keyword", species);
9190
pagination.addFilterOption("evidenceCodes.abbreviation", evidenceCode);
9291
pagination.addFilterOption("generatedRelationString.keyword", associationType);
9392
pagination.addFilterOption("diseaseQualifiers.keyword", diseaseQualifier);
@@ -256,7 +255,7 @@ public JsonResultResponse<GeneDiseaseAnnotationDocument> getDiseaseAnnotationsBy
256255
pagination.addFilterOption("subject.curie", geneID);
257256
}
258257
if (species != null) {
259-
pagination.addFilterOption("subject.taxon.species.name.keyword", species);
258+
pagination.addFilterOption("subject.taxon.species.fullName.keyword", species);
260259
}
261260

262261

@@ -300,7 +299,7 @@ public JsonResultResponse<AGMDiseaseAnnotationDocument> getDiseaseAnnotationsFor
300299
long startTime = System.currentTimeMillis();
301300
Pagination pagination = new Pagination(page, limit, sortBy, asc);
302301
pagination.addFilterOption("subject.agmFullName.displayText", modelName);
303-
pagination.addFilterOption("subject.taxon.name.keyword", species);
302+
pagination.addFilterOption("subject.taxon.species.fullName.keyword", species);
304303
pagination.addFilterOption("evidenceCodes.abbreviation", evidenceCode);
305304
pagination.addFilterOption("generatedRelationString.keyword", associationType);
306305
pagination.addFilterOption("conditionModifierAggregated", conditionModifier);
@@ -414,14 +413,7 @@ private JsonResultResponse<GeneDiseaseAnnotationDocument> getDiseaseAnnotationsR
414413
pagination.addFilterOption("primaryAnnotations.with.geneSymbol.displayText", basedOnGeneSymbol);
415414
pagination.addFilterOption("primaryAnnotations.dataProvider.abbreviation OR primaryAnnotations.secondaryDataProvider.abbreviation", filterSource);
416415

417-
// TODO: remove when SC data is fixed:
418-
if (filterSpecies != null) {
419-
if (filterSpecies.equals("Saccharomyces cerevisiae")) {
420-
pagination.addFilterOption("subject.taxon.name.keyword", "Saccharomyces cerevisiae S288C");
421-
} else {
422-
pagination.addFilterOption("subject.taxon.name.keyword", filterSpecies);
423-
}
424-
}
416+
pagination.addFilterOption("subject.taxon.species.fullName.keyword", filterSpecies);
425417

426418
if (pagination.hasErrors()) {
427419
RestErrorMessage message = new RestErrorMessage();

‎agr_api/src/main/java/org/alliancegenome/api/controller/ExpressionController.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -78,7 +78,7 @@ public JsonResultResponse<GeneExpressionDocument> getExpressionAnnotations(
7878
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) {
7979
long startTime = System.currentTimeMillis();
8080
Pagination pagination = new Pagination(page, limit, sortBy, asc);
81-
pagination.addFilterOption("geneExpressionAnnotation.expressionAnnotationSubject.taxon.name", filterSpecies);
81+
pagination.addFilterOption("geneExpressionAnnotation.expressionAnnotationSubject.taxon.species.fullName.keyword", filterSpecies);
8282
pagination.addFilterOption("geneExpressionAnnotation.expressionAnnotationSubject.geneSymbol.displayText", filterGene);
8383
pagination.addFilterOption("geneExpressionAnnotation.whereExpressedStatement", filterLocation);
8484
pagination.addFilterOption("geneExpressionAnnotation.whenExpressedStageName", filterStage);

‎agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java‎

Lines changed: 5 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -226,13 +226,7 @@ public JsonResultResponse<GeneGeneticInteractionDocument> getGeneticInteractions
226226
pagination.addFilterOption("geneGeneticInteraction.interactorBGeneticPerturbation.alleleSymbol.displayText", interactorGeneticPerturbation);
227227
pagination.addFilterOption("geneGeneticInteraction.phenotypesOrTraits", phenotypes);
228228
pagination.addFilterOption("geneGeneticInteraction.interactionType.name.keyword", interactionType);
229-
if (interactorSpecies != null) {
230-
if (interactorSpecies.equals("Saccharomyces cerevisiae")) {
231-
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.taxon.name.keyword", "Saccharomyces cerevisiae S288C");
232-
} else {
233-
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.taxon.name.keyword", interactorSpecies);
234-
}
235-
}
229+
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.taxon.species.fullName.keyword", interactorSpecies);
236230
// Todo: needs to be made generic
237231
// pagination.validateFilterValues(info.getQueryParameters());
238232
if (pagination.hasErrors()) {
@@ -269,13 +263,7 @@ public Response getGeneticInteractionsDownload(String id, String sortBy, String
269263
pagination.addFilterOption("geneGeneticInteraction.interactorBGeneticPerturbation.alleleSymbol.displayText", interactorGeneticPerturbation);
270264
pagination.addFilterOption("geneGeneticInteraction.phenotypesOrTraits", phenotypes);
271265
pagination.addFilterOption("geneGeneticInteraction.interactionType.name.keyword", interactionType);
272-
if (interactorSpecies != null) {
273-
if (interactorSpecies.equals("Saccharomyces cerevisiae")) {
274-
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.taxon.name.keyword", "Saccharomyces cerevisiae S288C");
275-
} else {
276-
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.taxon.name.keyword", interactorSpecies);
277-
}
278-
}
266+
pagination.addFilterOption("geneGeneticInteraction.geneGeneAssociationObject.taxon.species.fullName.keyword", interactorSpecies);
279267

280268
JsonResultResponse<GeneGeneticInteractionDocument> interactions = geneService.getGeneticInteractions(id, pagination);
281269

@@ -298,13 +286,7 @@ public JsonResultResponse<GeneMolecularInteractionDocument> getMolecularInteract
298286
pagination.addFilterOption("geneMolecularInteraction.evidence.referenceID", reference);
299287
pagination.addFilterOption("geneMolecularInteraction.interactorBType.name.keyword", interactorMoleculeType);
300288
pagination.addFilterOption("geneMolecularInteraction.detectionMethod.name.keyword", detectionMethod);
301-
if (interactorSpecies != null) {
302-
if (interactorSpecies.equals("Saccharomyces cerevisiae")) {
303-
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.taxon.name.keyword", "Saccharomyces cerevisiae S288C");
304-
} else {
305-
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.taxon.name.keyword", interactorSpecies);
306-
}
307-
}
289+
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.taxon.species.fullName.keyword", interactorSpecies);
308290
// Todo: needs to be made generic
309291
// pagination.validateFilterValues(info.getQueryParameters());
310292
if (pagination.hasErrors()) {
@@ -337,13 +319,7 @@ public Response getMolecularInteractionsDownload(String id, String sortBy, Strin
337319
pagination.addFilterOption("geneMolecularInteraction.evidence.referenceID", reference);
338320
pagination.addFilterOption("geneMolecularInteraction.interactorBType.name.keyword", interactorMoleculeType);
339321
pagination.addFilterOption("geneMolecularInteraction.detectionMethod.name.keyword", detectionMethod);
340-
if (interactorSpecies != null) {
341-
if (interactorSpecies.equals("Saccharomyces cerevisiae")) {
342-
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.taxon.name.keyword", "Saccharomyces cerevisiae S288C");
343-
} else {
344-
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.taxon.name.keyword", interactorSpecies);
345-
}
346-
}
322+
pagination.addFilterOption("geneMolecularInteraction.geneGeneAssociationObject.taxon.species.fullName.keyword", interactorSpecies);
347323
JsonResultResponse<GeneMolecularInteractionDocument> interactions = geneService.getMolecularInteractions(id, pagination);
348324

349325
Response.ResponseBuilder responseBuilder = Response.ok(molecularInteractionTranslator.getAllRows(interactions.getResults()));
@@ -482,7 +458,7 @@ public JsonResultResponse<GeneTransgenicAlleleSummaryDocument> getTransgenicAlle
482458
sortBy = "transgenicAllele";
483459
}
484460
Pagination pagination = new Pagination(page, limit, sortBy, null);
485-
pagination.addFilterOption("alleleDocument.allele.taxon.name", species);
461+
pagination.addFilterOption("alleleDocument.allele.taxon.species.fullName.keyword", species);
486462
pagination.addFilterOption("alleleDocument.allele.alleleSymbol.formatText", alleleSymbol);
487463
pagination.addFilterOption("alleleDocument.transgenicAlleleConstructs.construct.constructSymbol.formatText", constructSymbol);
488464
pagination.addFilterOption("alleleDocument.transgenicAlleleConstructs.regulatoryGenes.geneSymbol.formatText", constructRegulatedGene);

‎agr_api/src/main/java/org/alliancegenome/api/service/DiseaseESService.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -109,7 +109,7 @@ private Map<String, Object> getSupplementalData(String focusTaxonId, boolean use
109109
// create histogram of select columns of unfiltered query
110110
Map<String, String> aggregationFields = new HashMap<>();
111111
if (useSpeciesAggregation) {
112-
aggregationFields.put("subject.taxon.name.keyword", "species");
112+
aggregationFields.put("subject.taxon.species.fullName.keyword", "species");
113113
}
114114
aggregationFields.put("generatedRelationString.keyword", "associationType");
115115
aggregationFields.put("diseaseQualifiers.keyword", "diseaseQualifiers");
@@ -277,7 +277,7 @@ public JsonResultResponse<GeneDiseaseAnnotationDocument> getDiseaseAnnotationsWi
277277
sortingSetMap.put("default", List.of("viaOrthologyOrder", "phylogeneticSortingIndex", "subject.geneSymbol.displayText.sort"));
278278
sortingSetMap.put("gene", List.of("subject.geneSymbol.displayText.sort", "phylogeneticSortingIndex"));
279279
sortingSetMap.put("disease", List.of("object.name.sort", "phylogeneticSortingIndex", "subject.geneSymbol.displayText.sort"));
280-
sortingSetMap.put("species", List.of("subject.taxon.name.keyword", "subject.geneSymbol.displayText.sort"));
280+
sortingSetMap.put("species", List.of("subject.taxon.species.fullName.keyword", "subject.geneSymbol.displayText.sort"));
281281

282282
LinkedHashMap<String, SortOrder> sortingMap = new LinkedHashMap<>();
283283

@@ -324,7 +324,7 @@ public JsonResultResponse<AGMDiseaseAnnotationDocument> getDiseaseAnnotationsWit
324324
sortingSetMap.put("default", List.of("phylogeneticSortingIndex", "subject.name.sort"));
325325
sortingSetMap.put("model", List.of("subject.name.sort", "phylogeneticSortingIndex"));
326326
sortingSetMap.put("disease", List.of("object.name.sort", "phylogeneticSortingIndex", "subject.name.sort"));
327-
sortingSetMap.put("species", List.of("subject.taxon.name.keyword", "subject.name.sort"));
327+
sortingSetMap.put("species", List.of("subject.taxon.species.fullName.keyword", "subject.name.sort"));
328328

329329
LinkedHashMap<String, SortOrder> sortingMap = new LinkedHashMap<>();
330330

@@ -372,7 +372,7 @@ public JsonResultResponse<AlleleDiseaseAnnotationDocument> getDiseaseAnnotations
372372
sortingSetMap.put("default", List.of("phylogeneticSortingIndex", "subject.alleleSymbol.displayText.sort"));
373373
sortingSetMap.put("allele", List.of("subject.alleleSymbol.displayText.sort", "phylogeneticSortingIndex"));
374374
sortingSetMap.put("disease", List.of("object.name.sort", "phylogeneticSortingIndex", "subject.alleleSymbol.displayText.sort"));
375-
sortingSetMap.put("species", List.of("subject.taxon.name.keyword", "subject.alleleSymbol.displayText.sort"));
375+
sortingSetMap.put("species", List.of("subject.taxon.species.fullName.keyword", "subject.alleleSymbol.displayText.sort"));
376376

377377
LinkedHashMap<String, SortOrder> sortingMap = new LinkedHashMap<>();
378378

‎agr_api/src/main/java/org/alliancegenome/api/service/ExpressionESService.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -73,7 +73,7 @@ private LinkedHashMap<String, SortOrder> getExpressionSortOrders(Pagination pagi
7373
LinkedHashMap<String, SortOrder> sortingMap = new LinkedHashMap<>();
7474
LinkedHashMap<String, String> sortingSetMap = new LinkedHashMap<>();
7575

76-
sortingSetMap.put("species", "geneExpressionAnnotation.expressionAnnotationSubject.taxon.name.keyword");
76+
sortingSetMap.put("species", "geneExpressionAnnotation.expressionAnnotationSubject.taxon.species.fullName.keyword");
7777
sortingSetMap.put("gene", "geneExpressionAnnotation.expressionAnnotationSubject.geneSymbol.displayText.sort");
7878
sortingSetMap.put("location", "geneExpressionAnnotation.whereExpressedStatement.sort");
7979
sortingSetMap.put("stage", "geneExpressionAnnotation.whenExpressedStageName.sort");
@@ -131,7 +131,7 @@ private LinkedHashMap<String, SortOrder> getExpressionSortOrders(Pagination pagi
131131
private Map<String, Object> getSupplementalData(BoolQueryBuilder unfilteredQuery) {
132132

133133
Map<String, String> aggregationFields = new HashMap<>();
134-
aggregationFields.put("geneExpressionAnnotation.expressionAnnotationSubject.taxon.name.keyword", "species");
134+
aggregationFields.put("geneExpressionAnnotation.expressionAnnotationSubject.taxon.species.fullName.keyword", "species");
135135
aggregationFields.put("geneExpressionAnnotation.whereExpressedStatement.keyword", "location");
136136
aggregationFields.put("geneExpressionAnnotation.whenExpressedStageName.keyword", "stage");
137137
aggregationFields.put("geneExpressionAnnotation.expressionAssayUsed.name.keyword", "assay");

‎agr_api/src/main/java/org/alliancegenome/api/service/GeneService.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -156,7 +156,7 @@ private Map<String, Object> getGeneticInteractionSupplementalData(BoolQueryBuild
156156
aggregationFields.put("geneGeneticInteraction.interactorARole.name.keyword", "filter.role");
157157
aggregationFields.put("geneGeneticInteraction.interactorBRole.name.keyword", "filter.interactorRole");
158158
aggregationFields.put("geneGeneticInteraction.interactionType.name.keyword", "filter.interactionType");
159-
aggregationFields.put("geneGeneticInteraction.geneGeneAssociationObject.taxon.name.keyword", "filter.interactorSpecies");
159+
aggregationFields.put("geneGeneticInteraction.geneGeneAssociationObject.taxon.species.fullName.keyword", "filter.interactorSpecies");
160160
return getInteractionSupplementalData(aggregationFields, unfilteredQuery);
161161
}
162162

@@ -165,7 +165,7 @@ private Map<String, Object> getMolecularInteractionSupplementalData(BoolQueryBui
165165
aggregationFields.put("geneMolecularInteraction.interactorBType.name.keyword", "filter.interactorMoleculeType");
166166
aggregationFields.put("geneMolecularInteraction.interactorAType.name.keyword", "filter.moleculeType");
167167
aggregationFields.put("geneMolecularInteraction.detectionMethod.name.keyword", "filter.detectionMethod");
168-
aggregationFields.put("geneMolecularInteraction.geneGeneAssociationObject.taxon.name.keyword", "filter.interactorSpecies");
168+
aggregationFields.put("geneMolecularInteraction.geneGeneAssociationObject.taxon.species.fullName.keyword", "filter.interactorSpecies");
169169
return getInteractionSupplementalData(aggregationFields, unfilteredQuery);
170170
}
171171

‎agr_api/src/main/java/org/alliancegenome/api/service/TransgenicAlleleESService.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -27,7 +27,7 @@ public JsonResultResponse<GeneTransgenicAlleleSummaryDocument> getTransgenicAlle
2727
BoolQueryBuilder query = getBaseModelQuery(List.of(geneId), false, "transgenic_allele_annotations");
2828

2929
JsonResultResponse<GeneTransgenicAlleleSummaryDocument> ret = new JsonResultResponse<>();
30-
Map<String, String> aggregationFields = Map.of("alleleDocument.allele.taxon.name.keyword", "species");
30+
Map<String, String> aggregationFields = Map.of("alleleDocument.allele.taxon.species.fullName.keyword", "species");
3131
ret.setSupplementalData(getSupplementalData(geneId, true, debug, query, aggregationFields));
3232

3333
// add table filter

‎agr_java_core/src/main/java/org/alliancegenome/es/index/site/schema/Mapping.java‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -137,6 +137,7 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
137137
new FieldBuilder(builder, "object.name", "text").keyword().sort().build(); // gene_disease_annotation, allele_disease_annotation, agm_disease_annotation
138138
new FieldBuilder(builder, "object.curie", "text").keyword().sort().build(); // gene_disease_annotation, allele_disease_annotation, agm_disease_annotation
139139
new FieldBuilder(builder, "subject.primaryExternalId", "text").keyword().sort().build(); // gene_disease_annotation, allele_disease_annotation, agm_disease_annotation
140+
new FieldBuilder(builder, "subject.taxon.species.fullName", "text").keyword().sort().build(); // gene_disease_annotation, allele_disease_annotation, agm_disease_annotation
140141

141142
new FieldBuilder(builder, "anatomicalExpressionSlim", "text").keyword().build(); // gene, dataset
142143
new FieldBuilder(builder, "whereExpressed", "text").keyword().build(); // gene, dataset
@@ -148,6 +149,7 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
148149
new FieldBuilder(builder, "model.agmFullName.displayText", "text").keyword().sort().build(); //
149150
new FieldBuilder(builder, "model.agmFullName.formatText", "text").keyword().sort().build(); //
150151
new FieldBuilder(builder, "alleleDocument.allele.alleleSymbol.formatText", "text").keyword().sort().build(); //
152+
new FieldBuilder(builder, "alleleDocument.allele.taxon.species.fullName", "text").keyword().sort().build(); //
151153
new FieldBuilder(builder, "alleleDocument.phylogeneticSortingIndex", "long").keyword().sort().build(); //
152154
new FieldBuilder(builder, "definition", "text").standardText().build(); // go, disease
153155

@@ -193,6 +195,7 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
193195
builder.endObject();
194196
new FieldBuilder(builder, "geneMolecularInteraction.geneGeneAssociationObject.geneSymbol.displayText", "text").keyword().sort().build();
195197
new FieldBuilder(builder, "geneMolecularInteraction.geneGeneAssociationObject.taxon.name", "text").keyword().sort().build();
198+
new FieldBuilder(builder, "geneMolecularInteraction.geneGeneAssociationObject.taxon.species.fullName", "text").keyword().sort().build();
196199
new FieldBuilder(builder, "geneMolecularInteraction.geneAssociationSubject.curie", "text").keyword().build();
197200
new FieldBuilder(builder, "geneMolecularInteraction.geneAssociationSubject.primaryExternalId", "text").keyword().build();
198201
new FieldBuilder(builder, "geneMolecularInteraction.interactorAType.name", "text").keyword().sort().build();
@@ -211,6 +214,7 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
211214
builder.endObject();
212215
new FieldBuilder(builder, "geneGeneticInteraction.geneGeneAssociationObject.geneSymbol.displayText", "text").keyword().sort().build();
213216
new FieldBuilder(builder, "geneGeneticInteraction.geneGeneAssociationObject.taxon.name", "text").keyword().sort().build();
217+
new FieldBuilder(builder, "geneGeneticInteraction.geneGeneAssociationObject.taxon.species.fullName", "text").keyword().sort().build();
214218
new FieldBuilder(builder, "geneGeneticInteraction.geneAssociationSubject.curie", "text").keyword().build();
215219
new FieldBuilder(builder, "geneGeneticInteraction.geneAssociationSubject.primaryExternalId", "text").keyword().build();
216220
new FieldBuilder(builder, "geneGeneticInteraction.interactorARole.name", "text").keyword().build();
@@ -255,6 +259,7 @@ protected void buildSharedSearchableDocumentMappings() throws IOException {
255259
new FieldBuilder(builder, "geneExpressionAnnotation.expressionAnnotationSubject.geneSymbol.displayText", "text").keyword().sort().build();
256260
new FieldBuilder(builder, "geneExpressionAnnotation.expressionAnnotationSubject.primaryExternalId", "text").keyword().build();
257261
new FieldBuilder(builder, "geneExpressionAnnotation.expressionAnnotationSubject.taxon.name", "text").keyword().sort().build();
262+
new FieldBuilder(builder, "geneExpressionAnnotation.expressionAnnotationSubject.taxon.species.fullName", "text").keyword().sort().build();
258263
new FieldBuilder(builder, "geneExpressionAnnotation.whereExpressedStatement", "text").keyword().sort().build();
259264
new FieldBuilder(builder, "geneExpressionAnnotation.whenExpressedStageName", "text").keyword().sort().build();
260265
new FieldBuilder(builder, "geneExpressionAnnotation.expressionAssayUsed.name", "text").keyword().sort().build();

‎pom.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,7 @@
2323
<maven-checkstyle-plugin.version>3.3.1</maven-checkstyle-plugin.version>
2424
<checkstyle.version>10.17.0</checkstyle.version>
2525
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
26-
<curation.version>v0.47.21</curation.version>
26+
<curation.version>v0.47.24</curation.version>
2727
</properties>
2828
<dependencyManagement>
2929
<dependencies>

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