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SCRUM-3998 add genetic entity info for allele and gene phenotype anno… #1251

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Merged
cmpich merged 2 commits into from
Mar 4, 2025
Merged

SCRUM-3998 add genetic entity info for allele and gene phenotype anno… #1251

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SCRUM-3998 add genetic entity info for allele and gene phenotype anno…
cmpich Mar 4, 2025
8a852c7
SCRUM-3998 remove unused import
cmpich Mar 4, 2025
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12 changes: 12 additions & 0 deletions ...main/java/org/alliancegenome/core/translators/tdf/PhenotypeAnnotationToTdfTranslator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@

import org.alliancegenome.api.entity.PhenotypeAnnotationDocument;
import org.alliancegenome.curation_api.model.entities.AGMPhenotypeAnnotation;
import org.alliancegenome.curation_api.model.entities.AllelePhenotypeAnnotation;
import org.alliancegenome.curation_api.model.entities.GenePhenotypeAnnotation;
import org.alliancegenome.curation_api.model.entities.PhenotypeAnnotation;
import org.apache.commons.collections.CollectionUtils;

Expand Down Expand Up @@ -43,6 +45,16 @@ private PhenotypeDownloadRow getPhenotypeDownloadRow(PhenotypeAnnotation annotat
row.setGeneticEntityName(annot.getPhenotypeAnnotationSubject().getName());
row.setGeneticEntityType(annot.getPhenotypeAnnotationSubject().getSubtype().getName());
}
if (annotation instanceof AllelePhenotypeAnnotation annot) {
row.setGeneticEntityID(annot.getPhenotypeAnnotationSubject().getPrimaryExternalId());
row.setGeneticEntityName(annot.getPhenotypeAnnotationSubject().getAlleleSymbol().getDisplayText());
row.setGeneticEntityType("allele");
}
if (annotation instanceof GenePhenotypeAnnotation annot) {
row.setGeneticEntityID(annot.getPhenotypeAnnotationSubject().getPrimaryExternalId());
row.setGeneticEntityName(annot.getPhenotypeAnnotationSubject().getGeneSymbol().getDisplayText());
row.setGeneticEntityType("gene");
}
return row;
}

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