feature-improveclinical: still adapting ClinVarIndexter to the new EvidenceEntry model
@@ -278,15 +278,17 @@ public class ClinVarIndexer extends ClinicalIndexer {
}
List<AlleleOrigin> alleleOrigin = getAlleleOriginList(originSet);
+ List<HeritableTrait> heritableTraitList = getHeritableTrait(publicSet, traitsToEfoTermsMap);
+
// FIXME: commented to enable compiling for priesgo. Must be uncommented and fixed
-// EvidenceEntry evidenceEntry = new EvidenceEntry(evidenceSource, null, xxxxx,
-// "https://www.ncbi.nlm.nih.gov/clinvar/" + accession, accession,
-// !alleleOrigin.isEmpty() ? alleleOrigin : null, heritableTraitList, genomicFeatureList,
-// variantClassification, null,
-// null, consistencyStatus, null, null, null,
-// null, additionalProperties, null);
-//
-// evidenceEntryList.add(evidenceEntry);
+ EvidenceEntry evidenceEntry = new EvidenceEntry(evidenceSource, null, null,
+ "https://www.ncbi.nlm.nih.gov/clinvar/" + accession, accession,
+ !alleleOrigin.isEmpty() ? alleleOrigin : null, heritableTraitList, genomicFeatureList,
+ variantClassification, null,
+ null, consistencyStatus, null, null, null,
+ null, additionalProperties, null);
+
+ evidenceEntryList.add(evidenceEntry);
}
@@ -387,7 +389,7 @@ public class ClinVarIndexer extends ClinicalIndexer {
}
}
- private List<String> getDisease(PublicSetType publicSet, Map<String, EFO> traitsToEfoTermsMap) {
+ private List<String> getHeritableTrait(PublicSetType publicSet, Map<String, EFO> traitsToEfoTermsMap) {
Set<String> diseaseList = new HashSet<>();
for (TraitType trait : publicSet.getReferenceClinVarAssertion().getTraitSet().getTrait()) {
// if (!trait.getType().equalsIgnoreCase("disease")) {
