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Merge branch 'master' into rfc85-dynamic-virtual-study
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@forus
forus authored Oct 28, 2024
2 parents 4b49f4f + 8d6511c commit 3287498
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25 changes: 0 additions & 25 deletions end-to-end-test/remote/specs/core/comparisonTab.screenshot.spec.js
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Expand Up @@ -408,31 +408,6 @@ describe('results view comparison tab screenshot tests', () => {
);
assertScreenShotMatch(res);
});

it('results view comparison tab microbiome signature tab two groups', async () => {
await clickElement('button[data-test="groupSelectorButtonBRAF"]', {
timeout: 20000,
});

await (
await getElement(
'div[data-test="GroupComparisonMethylationEnrichments"]'
)
).waitForDisplayed({ timeout: 10000 });
await waitForElementDisplayed('b=RER1', { timeout: 10000 });
await clickElement('b=RER1');
await (await getElement('body')).moveTo({
x:0, y:0
});
const res = await browser.checkElement(
'.msk-tab:not(.hiddenByPosition)',
'',
{
hide: ['.qtip'],
}
);
assertScreenShotMatch(res);
});
});

describe('delete group from session', () => {
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16 changes: 8 additions & 8 deletions package.json
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@@ -1,7 +1,7 @@
{
"name": "cbioportal-frontend",
"private": true,
"version": "3.3.285",
"version": "3.3.286",
"workspaces": {
"packages": [
".",
Expand Down Expand Up @@ -88,7 +88,7 @@
"@babel/plugin-transform-modules-commonjs": "^7.4.4",
"@babel/preset-env": "^7.4.4",
"@babel/preset-react": "^7.0.0",
"@datadog/browser-logs": "^5.4.0",
"@datadog/browser-logs": "^5.28.0",
"@rollup/plugin-commonjs": "^22.0.0",
"@rollup/plugin-image": "^2.1.1",
"@rollup/plugin-json": "^4.1.0",
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": "^0.3.85",
"cbioportal-frontend-commons": "^0.5.69",
"cbioportal-clinical-timeline": "^0.3.86",
"cbioportal-frontend-commons": "^0.5.70",
"cbioportal-ts-api-client": "^0.9.73",
"cbioportal-utils": "^0.3.43",
"cbioportal-utils": "^0.3.44",
"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": "^1.1.33",
"genome-nexus-ts-api-client": "^1.1.34",
"git-revision-webpack-plugin": "^5.0.0",
"history": "4.10.1",
"html-webpack-plugin": "^5.3.2",
Expand Down Expand Up @@ -227,7 +227,7 @@
"mobx-utils": "6.0.1",
"numeral": "^2.0.6",
"object-sizeof": "^1.2.0",
"oncokb-frontend-commons": "^0.0.27",
"oncokb-frontend-commons": "^0.0.28",
"oncokb-styles": "~1.4.2",
"oncokb-ts-api-client": "^1.3.6",
"oncoprintjs": "^6.0.6",
Expand Down Expand Up @@ -272,7 +272,7 @@
"react-markdown": "^7.0.1",
"react-mfb": "^0.6.0",
"react-motion": "^0.4.7",
"react-mutation-mapper": "^0.8.113",
"react-mutation-mapper": "^0.8.114",
"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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@@ -1,7 +1,7 @@
{
"name": "cbioportal-clinical-timeline",
"description": "cBioPortal Clinical Timeline",
"version": "0.3.85",
"version": "0.3.86",
"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": "^0.5.69",
"cbioportal-frontend-commons": "^0.5.70",
"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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@@ -1,7 +1,7 @@
{
"name": "cbioportal-frontend-commons",
"description": "cBioPortal Frontend Modules",
"version": "0.5.69",
"version": "0.5.70",
"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": "^0.3.43",
"cbioportal-utils": "^0.3.44",
"classnames": "^2.2.5",
"jquery": "^3.2.1",
"juice": "^10.0.0",
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4 changes: 2 additions & 2 deletions packages/cbioportal-utils/package.json
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@@ -1,7 +1,7 @@
{
"name": "cbioportal-utils",
"description": "cBioPortal Utilities",
"version": "0.3.43",
"version": "0.3.44",
"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": "^1.1.33",
"genome-nexus-ts-api-client": "^1.1.34",
"lodash": "^4.17.15",
"oncokb-ts-api-client": "^1.3.6",
"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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@@ -1,7 +1,7 @@
{
"name": "genome-nexus-ts-api-client",
"description": "Genome Nexus API Client for TypeScript",
"version": "1.1.33",
"version": "1.1.34",
"main": "dist/index.js",
"module": "dist/index.es.js",
"jsnext:main": "dist/index.es.js",
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140 changes: 37 additions & 103 deletions packages/genome-nexus-ts-api-client/src/generated/GenomeNexusAPI-docs.json
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Expand Up @@ -2506,6 +2506,26 @@
}
}
},
"IntergenicConsequenceSummary": {
"type": "object",
"properties": {
"consequenceTerms": {
"type": "array",
"items": {
"type": "string"
}
},
"impact": {
"type": "string"
},
"variantAllele": {
"type": "string"
},
"variantClassification": {
"type": "string"
}
}
},
"IntergenicConsequences": {
"type": "object",
"required": [
Expand Down Expand Up @@ -2554,124 +2574,32 @@
},
"MutationAssessor": {
"type": "object",
"required": [
"input"
],
"properties": {
"codonStartPosition": {
"type": "string",
"description": "Codon start position"
},
"cosmicCount": {
"type": "integer",
"format": "int32",
"description": "Number of mutations in COSMIC for this protein"
},
"functionalImpact": {
"type": "string",
"description": "Functional impact"
"functionalImpactPrediction": {
"type": "string"
},
"functionalImpactScore": {
"type": "number",
"format": "double",
"description": "Functional impact score"
},
"hgvs": {
"hgvspShort": {
"type": "string"
},
"hugoSymbol": {
"type": "string",
"description": "Hugo gene symbol"
},
"input": {
"type": "string",
"description": "User-input variants"
},
"mappingIssue": {
"type": "string",
"description": "Mapping issue info"
},
"msaGaps": {
"type": "number",
"format": "double",
"description": "Portion of gaps in variant position in multiple sequence alignment"
},
"msaHeight": {
"mav": {
"type": "integer",
"format": "int32",
"description": "Number of diverse sequences in multiple sequence alignment (identical or highly similar sequences filtered out)"
},
"msaLink": {
"type": "string",
"description": "Link to multiple sequence alignment"
},
"pdbLink": {
"type": "string",
"description": "Link to 3d structure browser"
},
"referenceGenomeVariant": {
"type": "string",
"description": "Reference genome variant"
},
"referenceGenomeVariantType": {
"type": "string",
"description": "Reference genome variant type"
},
"refseqId": {
"type": "string",
"description": "Refseq protein ID"
},
"refseqPosition": {
"type": "integer",
"format": "int32",
"description": "Variant position in Refseq protein, can be different from the one in Uniprot"
"format": "int32"
},
"refseqResidue": {
"type": "string",
"description": "Reference residue in Refseq protein, can be different from the one in Uniprot"
"msa": {
"type": "string"
},
"snpCount": {
"sv": {
"type": "integer",
"format": "int32",
"description": "Number of SNPs in dbSNP for this protein"
"format": "int32"
},
"uniprotId": {
"type": "string",
"description": "Uniprot protein accession ID"
},
"uniprotPosition": {
"type": "integer",
"format": "int32",
"description": "Variant position in Uniprot protein, can be different from the one in Refseq"
},
"uniprotResidue": {
"type": "string",
"description": "Reference residue in Uniprot protein, can be different from the one in Refseq"
},
"variant": {
"type": "string",
"description": "Amino acid substitution"
},
"variantConservationScore": {
"type": "number",
"format": "double",
"description": "Variant conservation score"
},
"variantSpecificityScore": {
"type": "number",
"format": "double",
"description": "Variant specificity score"
}
}
},
"MutationAssessorAnnotation": {
"type": "object",
"properties": {
"annotation": {
"$ref": "#/definitions/MutationAssessor"
},
"license": {
"type": "string"
}
}
},
Expand Down Expand Up @@ -3676,8 +3604,8 @@
"description": "Most severe consequence"
},
"mutation_assessor": {
"description": "Mutation Assessor Annotation",
"$ref": "#/definitions/MutationAssessorAnnotation"
"description": "Mutation Assessor",
"$ref": "#/definitions/MutationAssessor"
},
"my_variant_info": {
"description": "My Variant Info Annotation",
Expand Down Expand Up @@ -3758,6 +3686,12 @@
"description": "Genomic location",
"$ref": "#/definitions/GenomicLocation"
},
"intergenicConsequenceSummaries": {
"type": "array",
"items": {
"$ref": "#/definitions/IntergenicConsequenceSummary"
}
},
"strandSign": {
"type": "string",
"description": "Strand (- or +)"
Expand Down
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