diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json index 3a0877e25a5..1c2683aeb99 100644 --- a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json +++ b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json @@ -3800,6 +3800,18 @@ } } }, + "VueReference": { + "type": "object", + "properties": { + "pubmedId": { + "type": "integer", + "format": "int32" + }, + "referenceText": { + "type": "string" + } + } + }, "Vues": { "type": "object", "properties": { @@ -3824,19 +3836,24 @@ "hugoGeneSymbol": { "type": "string" }, - "pubmedId": { - "type": "integer", - "format": "int32" - }, - "referenceText": { + "mutationOrigin": { "type": "string" }, + "references": { + "type": "array", + "items": { + "$ref": "#/definitions/VueReference" + } + }, "revisedProteinEffect": { "type": "string" }, "revisedVariantClassification": { "type": "string" }, + "revisedVariantClassificationStandard": { + "type": "string" + }, "transcriptId": { "type": "string" }, diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts index 693494137c9..58dba3d740f 100644 --- a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts +++ b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts @@ -1060,6 +1060,12 @@ export type Version = { 'version': string +}; +export type VueReference = { + 'pubmedId': number + + 'referenceText': string + }; export type Vues = { 'comment': string @@ -1076,14 +1082,16 @@ export type Vues = { 'hugoGeneSymbol': string - 'pubmedId': number + 'mutationOrigin': string - 'referenceText': string + 'references': Array < VueReference > 'revisedProteinEffect': string 'revisedVariantClassification': string + 'revisedVariantClassificationStandard': string + 'transcriptId': string 'variant': string diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json index 38a7c4faf11..9fa1a4d7329 100644 --- a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json +++ b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json @@ -2370,6 +2370,18 @@ } } }, + "VueReference": { + "type": "object", + "properties": { + "pubmedId": { + "type": "integer", + "format": "int32" + }, + "referenceText": { + "type": "string" + } + } + }, "Vues": { "type": "object", "properties": { @@ -2394,19 +2406,24 @@ "hugoGeneSymbol": { "type": "string" }, - "pubmedId": { - "type": "integer", - "format": "int32" - }, - "referenceText": { + "mutationOrigin": { "type": "string" }, + "references": { + "type": "array", + "items": { + "$ref": "#/definitions/VueReference" + } + }, "revisedProteinEffect": { "type": "string" }, "revisedVariantClassification": { "type": "string" }, + "revisedVariantClassificationStandard": { + "type": "string" + }, "transcriptId": { "type": "string" }, diff --git a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts index 134b2595298..3f0b07b07be 100644 --- a/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts +++ b/packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts @@ -614,6 +614,12 @@ export type Vcf = { 'ref': string +}; +export type VueReference = { + 'pubmedId': number + + 'referenceText': string + }; export type Vues = { 'comment': string @@ -630,14 +636,16 @@ export type Vues = { 'hugoGeneSymbol': string - 'pubmedId': number + 'mutationOrigin': string - 'referenceText': string + 'references': Array < VueReference > 'revisedProteinEffect': string 'revisedVariantClassification': string + 'revisedVariantClassificationStandard': string + 'transcriptId': string 'variant': string diff --git a/packages/react-mutation-mapper/src/component/revue/Revue.tsx b/packages/react-mutation-mapper/src/component/revue/Revue.tsx index 9966e702bbb..55036820d96 100644 --- a/packages/react-mutation-mapper/src/component/revue/Revue.tsx +++ b/packages/react-mutation-mapper/src/component/revue/Revue.tsx @@ -34,15 +34,18 @@ export const RevueTooltipContent: React.FunctionComponent<{ } {` (`} - { - - {props.vue.referenceText} - - } + {props.vue.references.map((reference, index) => ( + + + {reference.referenceText} + + {index < props.vue.references.length - 1 && ';'} + + ))} {`): `} {props.vue.revisedProteinEffect} diff --git a/src/shared/components/mutationTable/column/AnnotationColumnFormatter.tsx b/src/shared/components/mutationTable/column/AnnotationColumnFormatter.tsx index c4d471e1ab8..cd1131930e0 100644 --- a/src/shared/components/mutationTable/column/AnnotationColumnFormatter.tsx +++ b/src/shared/components/mutationTable/column/AnnotationColumnFormatter.tsx @@ -98,7 +98,18 @@ export default class AnnotationColumnFormatter { annotationDownloadContent.push( `reVUE: ${ annotationData.vue - ? `${annotationData.vue.comment},PubmedId:${annotationData.vue.pubmedId},PredictedEffect:${annotationData.vue.defaultEffect},ExperimentallyValidatedEffect:${annotationData.vue.revisedVariantClassification},RevisedProteinEffect:${annotationData.vue.revisedProteinEffect}` + ? `${ + annotationData.vue.comment + },PubmedId:${annotationData.vue.references + .map(reference => reference.pubmedId) + .join(';')},PredictedEffect:${ + annotationData.vue.defaultEffect + },ExperimentallyValidatedEffect:${ + annotationData.vue + .revisedVariantClassificationStandard + },RevisedProteinEffect:${ + annotationData.vue.revisedProteinEffect + }` : 'no' }` );