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Merge branch 'master' into fix-10375
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@7xuanlu
7xuanlu authored Jun 14, 2024
2 parents 350f297 + 418be26 commit f2ebca1
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Showing 24 changed files with 170 additions and 70 deletions.
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6 changes: 3 additions & 3 deletions end-to-end-test/remote/specs/core/groupComparisonLollipop.spec.js
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Original file line number Diff line number Diff line change
Expand Up @@ -908,7 +908,7 @@ describe('group comparison mutations tab tests', function() {

assert.equal(
getElementByTestHandle('LazyMobXTable_CountHeader').getText(),
'14 Mutations (page 1 of 1)'
'14 Mutations'
);

assert.equal(
Expand All @@ -921,7 +921,7 @@ describe('group comparison mutations tab tests', function() {

assert.equal(
getElementByTestHandle('LazyMobXTable_CountHeader').getText(),
'1 Mutation (page 1 of 1)'
'1 Mutation'
);

assert.equal(
Expand All @@ -934,7 +934,7 @@ describe('group comparison mutations tab tests', function() {

assert.equal(
getElementByTestHandle('LazyMobXTable_CountHeader').getText(),
'16 Mutations (page 1 of 1)'
'16 Mutations'
);

assert.equal(
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4 changes: 2 additions & 2 deletions end-to-end-test/remote/specs/core/screenshot.spec.js
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Original file line number Diff line number Diff line change
Expand Up @@ -270,10 +270,10 @@ describe('patient view page screenshot test', function() {
goToUrlAndSetLocalStorage(url);

// should show 0 mutations
$('.//*[text()[contains(.,"0 Mutations")]]').waitForExist();
$('span*=0 Mutations').waitForExist();

// should show 21.6% copy number altered in genomic overview
$('.//*[text()[contains(.,"21.6%")]]').waitForExist();
$('div*=21.6%').waitForExist();

// take screenshot
var res = browser.checkElement('#mainColumn', '', { hide: ['.qtip'] });
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14 changes: 7 additions & 7 deletions package.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"name": "cbioportal-frontend",
"private": true,
"version": "3.3.279",
"version": "3.3.280",
"workspaces": {
"packages": [
".",
Expand Down Expand Up @@ -159,10 +159,10 @@
"bootstrap-sass": "3.4.1",
"bowser": "^1.7.1",
"bundle-loader": "^0.5.4",
"cbioportal-clinical-timeline": "^0.3.81",
"cbioportal-frontend-commons": "^0.5.65",
"cbioportal-clinical-timeline": "^0.3.82",
"cbioportal-frontend-commons": "^0.5.66",
"cbioportal-ts-api-client": "^0.9.72",
"cbioportal-utils": "^0.3.40",
"cbioportal-utils": "^0.3.41",
"chart.js": "^2.6.0",
"classnames": "^2.2.5",
"clinical-timeline": "0.0.30",
Expand All @@ -189,7 +189,7 @@
"fmin": "^0.0.2",
"font-awesome": "^4.7.0",
"fork-ts-checker-webpack-plugin": "^6.3.3",
"genome-nexus-ts-api-client": "^1.1.31",
"genome-nexus-ts-api-client": "^1.1.32",
"git-revision-webpack-plugin": "^5.0.0",
"history": "4.10.1",
"html-webpack-plugin": "^5.3.2",
Expand Down Expand Up @@ -228,7 +228,7 @@
"mobx-utils": "6.0.1",
"numeral": "^2.0.6",
"object-sizeof": "^1.2.0",
"oncokb-frontend-commons": "^0.0.24",
"oncokb-frontend-commons": "^0.0.25",
"oncokb-styles": "~1.4.2",
"oncokb-ts-api-client": "^1.3.5",
"oncoprintjs": "^6.0.5",
Expand Down Expand Up @@ -273,7 +273,7 @@
"react-markdown": "^7.0.1",
"react-mfb": "^0.6.0",
"react-motion": "^0.4.7",
"react-mutation-mapper": "^0.8.108",
"react-mutation-mapper": "^0.8.109",
"react-overlays": "0.7.4",
"react-portal": "^4.2.0",
"react-rangeslider": "^2.1.0",
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4 changes: 2 additions & 2 deletions packages/cbioportal-clinical-timeline/package.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"name": "cbioportal-clinical-timeline",
"description": "cBioPortal Clinical Timeline",
"version": "0.3.81",
"version": "0.3.82",
"main": "dist/index.js",
"module": "dist/index.es.js",
"jsnext:main": "dist/index.es.js",
Expand Down Expand Up @@ -39,7 +39,7 @@
},
"dependencies": {
"autobind-decorator": "^2.1.0",
"cbioportal-frontend-commons": "^0.5.65",
"cbioportal-frontend-commons": "^0.5.66",
"lodash": "^4.17.11",
"react-bootstrap": "^0.31.5",
"react-overlays": "0.7.4",
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4 changes: 2 additions & 2 deletions packages/cbioportal-frontend-commons/package.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"name": "cbioportal-frontend-commons",
"description": "cBioPortal Frontend Modules",
"version": "0.5.65",
"version": "0.5.66",
"main": "dist/index.js",
"module": "dist/index.es.js",
"jsnext:main": "dist/index.es.js",
Expand Down Expand Up @@ -38,7 +38,7 @@
},
"dependencies": {
"autobind-decorator": "^2.1.0",
"cbioportal-utils": "^0.3.40",
"cbioportal-utils": "^0.3.41",
"classnames": "^2.2.5",
"jquery": "^3.2.1",
"lodash": "^4.17.15",
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4 changes: 2 additions & 2 deletions packages/cbioportal-utils/package.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"name": "cbioportal-utils",
"description": "cBioPortal Utilities",
"version": "0.3.40",
"version": "0.3.41",
"main": "dist/index.js",
"module": "dist/index.es.js",
"jsnext:main": "dist/index.es.js",
Expand Down Expand Up @@ -30,7 +30,7 @@
},
"dependencies": {
"buffer": "^6.0.3",
"genome-nexus-ts-api-client": "^1.1.31",
"genome-nexus-ts-api-client": "^1.1.32",
"lodash": "^4.17.15",
"oncokb-ts-api-client": "^1.3.5",
"superagent": "^3.8.3",
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2 changes: 1 addition & 1 deletion packages/genome-nexus-ts-api-client/package.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"name": "genome-nexus-ts-api-client",
"description": "Genome Nexus API Client for TypeScript",
"version": "1.1.31",
"version": "1.1.32",
"main": "dist/index.js",
"module": "dist/index.es.js",
"jsnext:main": "dist/index.es.js",
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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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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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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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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
4 changes: 2 additions & 2 deletions packages/oncokb-frontend-commons/package.json
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@@ -1,6 +1,6 @@
{
"name": "oncokb-frontend-commons",
"version": "0.0.24",
"version": "0.0.25",
"description": "OncoKB Frontend Modules",
"main": "dist/index.js",
"module": "dist/index.es.js",
Expand Down Expand Up @@ -35,7 +35,7 @@
"react-dom": "^15.0.0 || ^16.0.0"
},
"dependencies": {
"cbioportal-utils": "^0.3.40",
"cbioportal-utils": "^0.3.41",
"classnames": "^2.2.5",
"lodash": "^4.17.15",
"oncokb-styles": "~1.4.2",
Expand Down
10 changes: 5 additions & 5 deletions packages/react-mutation-mapper/package.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"name": "react-mutation-mapper",
"version": "0.8.108",
"version": "0.8.109",
"description": "Generic Mutation Mapper",
"main": "dist/index.js",
"module": "dist/index.es.js",
Expand Down Expand Up @@ -39,14 +39,14 @@
},
"dependencies": {
"autobind-decorator": "^2.1.0",
"cbioportal-frontend-commons": "^0.5.65",
"cbioportal-utils": "^0.3.40",
"cbioportal-frontend-commons": "^0.5.66",
"cbioportal-utils": "^0.3.41",
"classnames": "^2.2.5",
"genome-nexus-ts-api-client": "^1.1.31",
"genome-nexus-ts-api-client": "^1.1.32",
"jquery": "^3.2.1",
"lodash": "^4.17.15",
"memoize-weak-decorator": "^1.0.3",
"oncokb-frontend-commons": "^0.0.24",
"oncokb-frontend-commons": "^0.0.25",
"oncokb-styles": "~1.4.2",
"oncokb-ts-api-client": "^1.3.5",
"react-collapse": "^4.0.3",
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
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