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Update Genome Nexus API model and reVUE reference to fit new model #4919

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merged 5 commits into from
Jun 6, 2024
Merged

Update Genome Nexus API model and reVUE reference to fit new model #4919

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6468604
Update Genome Nexus API model
leexgh Jun 5, 2024
27f57f6
Update revue reference to fit new model
leexgh Jun 5, 2024
5c96a7a
Update API model
leexgh Jun 6, 2024
90886f0
Download data should use standard variant classification
leexgh Jun 6, 2024
9c9e869
Small changes to make code more readable
leexgh Jun 6, 2024
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27 changes: 22 additions & 5 deletions packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3800,6 +3800,18 @@
}
}
},
"VueReference": {
"type": "object",
"properties": {
"pubmedId": {
"type": "integer",
"format": "int32"
},
"referenceText": {
"type": "string"
}
}
},
"Vues": {
"type": "object",
"properties": {
Expand All @@ -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"
},
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12 changes: 10 additions & 2 deletions packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -1060,6 +1060,12 @@ export type Version = {

'version': string

};
export type VueReference = {
'pubmedId': number

'referenceText': string

};
export type Vues = {
'comment': string
Expand All @@ -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
Expand Down
27 changes: 22 additions & 5 deletions packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal-docs.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2370,6 +2370,18 @@
}
}
},
"VueReference": {
"type": "object",
"properties": {
"pubmedId": {
"type": "integer",
"format": "int32"
},
"referenceText": {
"type": "string"
}
}
},
"Vues": {
"type": "object",
"properties": {
Expand All @@ -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"
},
Expand Down
12 changes: 10 additions & 2 deletions packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPIInternal.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -614,6 +614,12 @@ export type Vcf = {

'ref': string

};
export type VueReference = {
'pubmedId': number

'referenceText': string

};
export type Vues = {
'comment': string
Expand All @@ -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
Expand Down
21 changes: 12 additions & 9 deletions packages/react-mutation-mapper/src/component/revue/Revue.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -34,15 +34,18 @@ export const RevueTooltipContent: React.FunctionComponent<{
</a>
}
{` (`}
{
<a
href={`https://pubmed.ncbi.nlm.nih.gov/${props.vue.pubmedId}/`}
rel="noopener noreferrer"
target="_blank"
>
{props.vue.referenceText}
</a>
}
{props.vue.references.map((reference, index) => (
<span key={index}>
<a
href={`https://pubmed.ncbi.nlm.nih.gov/${reference.pubmedId}/`}
rel="noopener noreferrer"
target="_blank"
>
{reference.referenceText}
</a>
{index < props.vue.references.length - 1 && ';'}
</span>
))}
{`): `}
<strong>{props.vue.revisedProteinEffect}</strong>
</li>
Expand Down
13 changes: 12 additions & 1 deletion src/shared/components/mutationTable/column/AnnotationColumnFormatter.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -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'
}`
);
Expand Down
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