Merge pull request #1221 from alliance-genome/SCRUM-4515

Fix for experimental conditions

Author: VarunReddy1111

agr_api/src/main/java/org/alliancegenome/api/translators/tdf/DiseaseAnnotationToTdfTranslator.java

@@ -235,6 +235,21 @@ private static void extracted(DiseaseAnnotationDocument annotation, org.alliance
 				row.setGeneticEntityType("Allele");
 			}
 		}
+		if (annotation.getCategory().equals("gene_disease_annotation") || annotation.getCategory().equals("allele_disease_annotation")) {
+			if (CollectionUtils.isNotEmpty(primaryAnnotation.getConditionRelations())) {
+				List<ConditionRelation> conditionModifiers = primaryAnnotation.getConditionRelations().stream()
+					.filter(conditionRelation -> conditionRelation.getConditionRelationType() != null)
+					.filter(conditionRelation -> conditionRelation.getConditionRelationType().getName().contains("has_condition")
+						|| conditionRelation.getConditionRelationType().getName().contains("induced")
+						|| conditionRelation.getConditionRelationType().getName().contains("ameliorated")
+						|| conditionRelation.getConditionRelationType().getName().contains("exacerbated")).toList();
+				List<String> experimentalConditionComponents = new ArrayList<>(conditionModifiers.stream().map(conditionRelation -> conditionRelation.getConditionRelationType().getName()).toList());
+				conditionModifiers.forEach(conditionRelation -> conditionRelation.getConditions().forEach(experimentalCondition -> {
+					experimentalConditionComponents.add(experimentalCondition.getConditionSummary());
+				}));
+				row.setExperimentalCondition(String.join(",", experimentalConditionComponents));
+			}
+		}
 		if (primaryAnnotation.getDiseaseGeneticModifierRelation() != null) {
 			row.setDiseaseGeneticModifierRelation(primaryAnnotation.getDiseaseGeneticModifierRelation().getName());
 		}
@@ -342,24 +357,6 @@ private DiseaseDownloadRow getBaseDiseaseDownloadRow(DiseaseAnnotationDocument a
 			row.setSource(sourceProvider);
 		}
 */
-		if (annotation.getCategory().equals("gene_disease_annotation") || annotation.getCategory().equals("allele_disease_annotation")) {
-			if (annotation.getPrimaryAnnotations() != null) {
-				for (org.alliancegenome.curation_api.model.entities.DiseaseAnnotation da : annotation.getPrimaryAnnotations()) {
-					if (CollectionUtils.isNotEmpty(da.getConditionRelations())) {
-						List<ConditionRelation> conditionModifiers = da.getConditionRelations().stream().filter(conditionRelation -> conditionRelation.getConditionRelationType() != null)
-							.filter(conditionRelation -> conditionRelation.getConditionRelationType().getName().contains("has_condition")
-							|| conditionRelation.getConditionRelationType().getName().contains("induced")
-							|| conditionRelation.getConditionRelationType().getName().contains("ameliorated")
-							|| conditionRelation.getConditionRelationType().getName().contains("exacerbated")).toList();
-						List<String> experimentalConditionComponents = new ArrayList<>(conditionModifiers.stream().map(conditionRelation -> conditionRelation.getConditionRelationType().getName()).toList());
-						conditionModifiers.forEach(conditionRelation -> conditionRelation.getConditions().forEach(experimentalCondition -> {
-							experimentalConditionComponents.add(experimentalCondition.getConditionSummary());
-						}));
-						row.setExperimentalCondition(String.join(",", experimentalConditionComponents));
-					}
-				}
-			}
-		}
 		StringJoiner evidenceJoiner = getStringJoiner(primaryAnnotation, org.alliancegenome.curation_api.model.entities.ontology.ECOTerm::getCurie);
 		row.setEvidenceCode(evidenceJoiner.toString());