From 1843dbb905222b27c2dc49fa211f858ef6d0061e Mon Sep 17 00:00:00 2001 From: Christian Pich Date: Tue, 4 Mar 2025 12:26:29 +0100 Subject: [PATCH 1/2] SCRUM-3998 add genetic entity info for allele and gene phenotype annotations --- .../tdf/PhenotypeAnnotationToTdfTranslator.java | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/PhenotypeAnnotationToTdfTranslator.java b/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/PhenotypeAnnotationToTdfTranslator.java index e378e3250..627a70a8b 100644 --- a/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/PhenotypeAnnotationToTdfTranslator.java +++ b/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/PhenotypeAnnotationToTdfTranslator.java @@ -1,7 +1,10 @@ package org.alliancegenome.core.translators.tdf; +import com.fasterxml.jackson.jakarta.rs.cfg.Annotations; 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; @@ -43,6 +46,16 @@ 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; } From 8a852c7a7257f6f1f65241a66d2dbed9083b75c2 Mon Sep 17 00:00:00 2001 From: Christian Pich Date: Tue, 4 Mar 2025 13:52:58 +0100 Subject: [PATCH 2/2] SCRUM-3998 remove unused import --- .../core/translators/tdf/PhenotypeAnnotationToTdfTranslator.java | 1 - 1 file changed, 1 deletion(-) diff --git a/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/PhenotypeAnnotationToTdfTranslator.java b/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/PhenotypeAnnotationToTdfTranslator.java index 627a70a8b..5eecfb258 100644 --- a/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/PhenotypeAnnotationToTdfTranslator.java +++ b/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/PhenotypeAnnotationToTdfTranslator.java @@ -1,6 +1,5 @@ package org.alliancegenome.core.translators.tdf; -import com.fasterxml.jackson.jakarta.rs.cfg.Annotations; import org.alliancegenome.api.entity.PhenotypeAnnotationDocument; import org.alliancegenome.curation_api.model.entities.AGMPhenotypeAnnotation; import org.alliancegenome.curation_api.model.entities.AllelePhenotypeAnnotation;