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Bump curation version to v0.26.0 (SCRUM-3367) #1130

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merged 4 commits into from
Oct 24, 2023
Merged

Bump curation version to v0.26.0 (SCRUM-3367) #1130

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c9df656
Bump curation version to v0.26.0 (SCRUM-3367)
mluypaert Oct 23, 2023
516062c
Refactored diseaseRelation to relation, SCRUM-3367
mluypaert Oct 23, 2023
9f32999
Refactored relationNegation to negationInclRelation, SCRUM-3367
mluypaert Oct 24, 2023
a0cb7cd
Refactored negationInclRelation to generatedRelationString, SCRUM-3367
mluypaert Oct 24, 2023
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2 changes: 1 addition & 1 deletion agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java
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Expand Up @@ -178,7 +178,7 @@ public JsonResultResponse<AlleleDiseaseAnnotationDocument> getDiseasePerAllele(S
pagination.addFilterOptions(filterOptions);
pagination.addFilterOption("object.name", diseaseTerm);
pagination.addFilterOption("evidenceCodes.abbreviation", evidenceCode);
pagination.addFilterOption("relationNegation.keyword", associationType);
pagination.addFilterOption("negationInclRelation.keyword", associationType);
pagination.addFilterOption("diseaseQualifiers.keyword", diseaseQualifier);
pagination.addFilterOption("pubmedPubModIDs", filterReference);
pagination.addFilterOption("primaryAnnotations.dataProvider.abbreviation", filterSource);
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2 changes: 1 addition & 1 deletion agr_api/src/main/java/org/alliancegenome/api/controller/DiseaseController.java
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Expand Up @@ -325,7 +325,7 @@ public JsonResultResponse<GeneDiseaseAnnotationDocument> getDiseaseAnnotationsRi
pagination.addFilterOptions(filterOptions);
pagination.addFilterOption("object.name", diseaseTerm);
pagination.addFilterOption("evidenceCodes.abbreviation", evidenceCode);
pagination.addFilterOption("relationNegation.keyword", associationType);
pagination.addFilterOption("negationInclRelation.keyword", associationType);
pagination.addFilterOption("diseaseQualifiers.keyword", diseaseQualifier);
pagination.addFilterOption("pubmedPubModIDs", filterReference);
pagination.addFilterOption("subject.geneSymbol.displayText", filterGene);
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2 changes: 1 addition & 1 deletion agr_api/src/main/java/org/alliancegenome/api/service/DiseaseESService.java
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Expand Up @@ -93,7 +93,7 @@ private Map<String, Object> getSupplementalData(String focusTaxonId, boolean deb
if (StringUtils.isNotEmpty(focusTaxonId)) {
aggregationFields.put("subject.taxon.name.keyword", "species");
}
aggregationFields.put("relationNegation.keyword", "associationType");
aggregationFields.put("negationInclRelation.keyword", "associationType");
aggregationFields.put("diseaseQualifiers.keyword", "diseaseQualifiers");
Map<String, List<String>> distinctFieldValueMap = getAggregations(unfilteredQuery, aggregationFields, focusTaxonId, debug);
Map<String, Object> supplementalData = new LinkedHashMap<>();
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2 changes: 1 addition & 1 deletion ...rc/main/java/org/alliancegenome/api/translators/tdf/DiseaseAnnotationToTdfTranslator.java
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Expand Up @@ -292,7 +292,7 @@ private DiseaseDownloadRow getDiseaseDownloadRow(DiseaseAnnotation annotation, P

private DiseaseDownloadRow getBaseDiseaseDownloadRow(GeneDiseaseAnnotationDocument annotation, org.alliancegenome.curation_api.model.entities.Gene homologousGene, org.alliancegenome.curation_api.model.entities.DiseaseAnnotation primaryAnnotation) {
DiseaseDownloadRow row = new DiseaseDownloadRow();
row.setAssociation(annotation.getRelationNegation());
row.setAssociation(annotation.getNegationInclRelation());
row.setDiseaseID(annotation.getObject().getCurie());
row.setDiseaseName(annotation.getObject().getName());
row.setSource(primaryAnnotation.getDataProviderString());
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10 changes: 5 additions & 5 deletions ...n/java/org/alliancegenome/indexer/indexers/curation/DiseaseAnnotationCurationIndexer.java
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Expand Up @@ -124,8 +124,8 @@ private List<GeneDiseaseAnnotationDocument> createGeneDiseaseAnnotationDocuments
HashMap<String, Integer> order = SpeciesType.getSpeciesOrderByTaxonID(entry.getValue().getLeft().getTaxon().getCurie());
gdad.setSpeciesOrder(order);
gdad.setRelation(relation);
String relationNegation = getRelationNegation(gdad.getRelation().getName(), da.getNegated());
gdad.setRelationNegation(relationNegation);
String negationInclRelation = getNegationInclRelation(gdad.getRelation().getName(), da.getNegated());
gdad.setNegationInclRelation(negationInclRelation);
gdad.setObject(da.getObject());
gdad.setParentSlimIDs(closureMap.get(da.getObject().getCurie()));
lookup.put(key, gdad);
Expand Down Expand Up @@ -161,7 +161,7 @@ private String getPubmedPubModID(Reference singleReference) {
return null;
}

private String getRelationNegation(String relation, Boolean negated) {
private String getNegationInclRelation(String relation, Boolean negated) {
if (!negated)
return relation;
return relation.replaceFirst("_", "_not_");
Expand All @@ -187,8 +187,8 @@ private List<AlleleDiseaseAnnotationDocument> createAlleleDiseaseAnnotationDocum
adad.setSpeciesOrder(order);
adad.setSubject(entry.getValue().getLeft());
adad.setRelation(da.getRelation());
String relationNegation = getRelationNegation(da.getRelation().getName(), da.getNegated());
adad.setRelationNegation(relationNegation);
String negationInclRelation = getNegationInclRelation(da.getRelation().getName(), da.getNegated());
adad.setNegationInclRelation(negationInclRelation);
adad.setObject(da.getObject());
lookup.put(key, adad);
}
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2 changes: 1 addition & 1 deletion agr_java_core/src/main/java/org/alliancegenome/api/entity/DiseaseAnnotationDocument.java
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Expand Up @@ -28,7 +28,7 @@ public class DiseaseAnnotationDocument extends SearchableItemDocument {
private Reference singleReference;
private Set<Reference> references;

private String relationNegation;
private String negationInclRelation;
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private Set<String> diseaseQualifiers;
private Set<String> pubmedPubModIDs;
private Set<String> parentSlimIDs;
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