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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("diseaseRelationNegation.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("diseaseRelationNegation.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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4 changes: 2 additions & 2 deletions agr_api/src/main/java/org/alliancegenome/api/rest/interfaces/AlleleRESTInterface.java
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Expand Up @@ -202,7 +202,7 @@ JsonResultResponse<AlleleDiseaseAnnotationDocument> getDiseasePerAllele(
@QueryParam("filter.geneticEntity") String geneticEntity,
@Parameter(in = ParameterIn.QUERY, name = "filter.geneticEntityType", description = "geneticEntityType", schema = @Schema(type = SchemaType.STRING))
@QueryParam("filter.geneticEntityType") String geneticEntityType,
@Parameter(in = ParameterIn.QUERY, name = "filter.diseaseRelation.name", description = "associationType", schema = @Schema(type = SchemaType.STRING))
@Parameter(in = ParameterIn.QUERY, name = "filter.relation.name", description = "associationType", schema = @Schema(type = SchemaType.STRING))
@QueryParam("filter.associationType") String associationType,
@Parameter(in = ParameterIn.QUERY, name = "filter.diseaseQualifier", description = "diseaseQualifier", schema = @Schema(type = SchemaType.STRING))
@QueryParam("filter.diseaseQualifier") String diseaseQualifier,
Expand Down Expand Up @@ -240,7 +240,7 @@ Response getDiseasePerAlleleDownload(
@QueryParam("filter.geneticEntity") String geneticEntity,
@Parameter(in = ParameterIn.QUERY, name = "filter.geneticEntityType", description = "geneticEntityType", schema = @Schema(type = SchemaType.STRING))
@QueryParam("filter.geneticEntityType") String geneticEntityType,
@Parameter(in = ParameterIn.QUERY, name = "filter.diseaseRelation.name", description = "associationType", schema = @Schema(type = SchemaType.STRING))
@Parameter(in = ParameterIn.QUERY, name = "filter.relation.name", description = "associationType", schema = @Schema(type = SchemaType.STRING))
@QueryParam("filter.associationType") String associationType,
@Parameter(in = ParameterIn.QUERY, name = "filter.diseaseQualifier", description = "diseaseQualifier", schema = @Schema(type = SchemaType.STRING))
@QueryParam("filter.diseaseQualifier") String diseaseQualifier,
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2 changes: 1 addition & 1 deletion agr_api/src/main/java/org/alliancegenome/api/rest/interfaces/DiseaseRESTInterface.java
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Expand Up @@ -376,7 +376,7 @@ JsonResultResponse<GeneDiseaseAnnotationDocument> getDiseaseAnnotationsRibbonDet
@QueryParam("filter.geneticEntity") String geneticEntity,
@Parameter(in = ParameterIn.QUERY, name = "filter.geneticEntityType", description = "geneticEntityType", schema = @Schema(type = SchemaType.STRING))
@QueryParam("filter.geneticEntityType") String geneticEntityType,
@Parameter(in = ParameterIn.QUERY, name = "filter.diseaseRelation.name", description = "associationType", schema = @Schema(type = SchemaType.STRING))
@Parameter(in = ParameterIn.QUERY, name = "filter.relation.name", description = "associationType", schema = @Schema(type = SchemaType.STRING))
@QueryParam("filter.associationType") String associationType,
@Parameter(in = ParameterIn.QUERY, name = "filter.diseaseQualifier", description = "diseaseQualifier", schema = @Schema(type = SchemaType.STRING))
@QueryParam("filter.diseaseQualifier") String diseaseQualifier,
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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("diseaseRelationNegation.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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4 changes: 2 additions & 2 deletions ...rc/main/java/org/alliancegenome/api/translators/tdf/DiseaseAnnotationToTdfTranslator.java
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Expand Up @@ -231,7 +231,7 @@ private static void extracted(GeneDiseaseAnnotationDocument annotation, org.alli
if (primaryAnnotation.getGeneticSex() != null) {
row.setGeneticSex(primaryAnnotation.getGeneticSex().getName());
}
row.setGeneticEntityAssociation(primaryAnnotation.getDiseaseRelation().getName());
row.setGeneticEntityAssociation(primaryAnnotation.getRelation().getName());
if (CollectionUtils.isNotEmpty(primaryAnnotation.getRelatedNotes())) {
row.setNote(primaryAnnotation.getRelatedNotes().stream().map(note -> {
if (note.getNoteType().getName().equals("disease_note")) {
Expand Down 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.getDiseaseRelationNegation());
row.setAssociation(annotation.getNegationInclRelation());
row.setDiseaseID(annotation.getObject().getCurie());
row.setDiseaseName(annotation.getObject().getName());
row.setSource(primaryAnnotation.getDataProviderString());
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30 changes: 15 additions & 15 deletions ...n/java/org/alliancegenome/indexer/indexers/curation/DiseaseAnnotationCurationIndexer.java
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Expand Up @@ -105,12 +105,12 @@ private List<GeneDiseaseAnnotationDocument> createGeneDiseaseAnnotationDocuments

for (DiseaseAnnotation da : entry.getValue().getRight()) {

VocabularyTerm diseaseRelation = vocabService.getVocabularyTerm("is_implicated_in");
VocabularyTerm relation = vocabService.getVocabularyTerm("is_implicated_in");
if (da instanceof GeneDiseaseAnnotation) {
diseaseRelation = da.getDiseaseRelation();
relation = da.getRelation();
}

String key = diseaseRelation.getName() + "_" + da.getObject().getName() + "_" + da.getNegated();
String key = relation.getName() + "_" + da.getObject().getName() + "_" + da.getNegated();
if (da.getWith() != null && da.getWith().size() > 0) {
List<String> withIds = da.getWith().stream().map(Gene::getCurie).collect(Collectors.toList());
Collections.sort(withIds);
Expand All @@ -123,9 +123,9 @@ private List<GeneDiseaseAnnotationDocument> createGeneDiseaseAnnotationDocuments
gdad.setSubject(entry.getValue().getLeft());
HashMap<String, Integer> order = SpeciesType.getSpeciesOrderByTaxonID(entry.getValue().getLeft().getTaxon().getCurie());
gdad.setSpeciesOrder(order);
gdad.setDiseaseRelation(diseaseRelation);
String diseaseRelationNegation = getDiseaseRelationNegation(gdad.getDiseaseRelation().getName(), da.getNegated());
gdad.setDiseaseRelationNegation(diseaseRelationNegation);
gdad.setRelation(relation);
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 @@ -161,10 +161,10 @@ private String getPubmedPubModID(Reference singleReference) {
return null;
}

private String getDiseaseRelationNegation(String diseaseRelation, Boolean negated) {
private String getNegationInclRelation(String relation, Boolean negated) {
if (!negated)
return diseaseRelation;
return diseaseRelation.replaceFirst("_", "_not_");
return relation;
return relation.replaceFirst("_", "_not_");
}

private List<AlleleDiseaseAnnotationDocument> createAlleleDiseaseAnnotationDocuments() {
Expand All @@ -178,17 +178,17 @@ private List<AlleleDiseaseAnnotationDocument> createAlleleDiseaseAnnotationDocum
HashMap<String, AlleleDiseaseAnnotationDocument> lookup = new HashMap<>();

for (DiseaseAnnotation da : entry.getValue().getRight()) {
String key = da.getDiseaseRelation().getName() + "_" + da.getObject().getName() + "_" + da.getNegated();
String key = da.getRelation().getName() + "_" + da.getObject().getName() + "_" + da.getNegated();
AlleleDiseaseAnnotationDocument adad = lookup.get(key);

if (adad == null) {
adad = new AlleleDiseaseAnnotationDocument();
HashMap<String, Integer> order = SpeciesType.getSpeciesOrderByTaxonID(entry.getValue().getLeft().getTaxon().getCurie());
adad.setSpeciesOrder(order);
adad.setSubject(entry.getValue().getLeft());
adad.setDiseaseRelation(da.getDiseaseRelation());
String diseaseRelationNegation = getDiseaseRelationNegation(da.getDiseaseRelation().getName(), da.getNegated());
adad.setDiseaseRelationNegation(diseaseRelationNegation);
adad.setRelation(da.getRelation());
String negationInclRelation = getNegationInclRelation(da.getRelation().getName(), da.getNegated());
adad.setNegationInclRelation(negationInclRelation);
adad.setObject(da.getObject());
lookup.put(key, adad);
}
Expand Down Expand Up @@ -220,15 +220,15 @@ private List<AGMDiseaseAnnotationDocument> createAGMDiseaseAnnotationDocuments()
HashMap<String, AGMDiseaseAnnotationDocument> lookup = new HashMap<>();

for (DiseaseAnnotation da : entry.getValue().getRight()) {
String key = da.getDiseaseRelation().getName() + "_" + da.getObject().getName() + "_" + da.getNegated();
String key = da.getRelation().getName() + "_" + da.getObject().getName() + "_" + da.getNegated();
AGMDiseaseAnnotationDocument adad = lookup.get(key);

if (adad == null) {
adad = new AGMDiseaseAnnotationDocument();
HashMap<String, Integer> order = SpeciesType.getSpeciesOrderByTaxonID(entry.getValue().getLeft().getTaxon().getCurie());
adad.setSpeciesOrder(order);
adad.setSubject(entry.getValue().getLeft());
adad.setDiseaseRelation(da.getDiseaseRelation());
adad.setRelation(da.getRelation());
adad.setObject(da.getObject());
lookup.put(key, adad);
}
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4 changes: 2 additions & 2 deletions agr_java_core/src/main/java/org/alliancegenome/api/entity/DiseaseAnnotationDocument.java
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Expand Up @@ -22,13 +22,13 @@
public class DiseaseAnnotationDocument extends SearchableItemDocument {

private String uniqueId;
private VocabularyTerm diseaseRelation;
private VocabularyTerm relation;
private DOTerm object;
private List<ECOTerm> evidenceCodes;
private Reference singleReference;
private Set<Reference> references;

private String diseaseRelationNegation;
private String negationInclRelation;
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private Set<String> diseaseQualifiers;
private Set<String> pubmedPubModIDs;
private Set<String> parentSlimIDs;
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2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -30,7 +30,7 @@
<quarkus.platform.artifact-id>quarkus-bom</quarkus.platform.artifact-id>
<quarkus.platform.group-id>io.quarkus.platform</quarkus.platform.group-id>
<quarkus.platform.version>${quarkus.version}</quarkus.platform.version>
<curation.version>v0.25.0</curation.version>
<curation.version>v0.26.0</curation.version>
<!-- <curation.version>0.0.0-SNAPSHOT</curation.version> -->
</properties>
<dependencyManagement>
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