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create react-variant-view package #3459

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merged 3 commits into from Oct 23, 2020
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@leexgh leexgh commented Oct 14, 2020

Fix cBioPortal/cbioportal#7946

react-variant-view package using for signal.
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https://www.npmjs.com/package/react-variant-view
This is a testing version, it has a lot of things could be cleaned up or updated

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leexgh commented Oct 14, 2020

Netlify shows error:

(plugin rpt2) Error: /opt/build/repo/packages/react-variant-view/src/util/AnnotationSummaryUtil.ts(9,9): semantic error TS2739: Type '{ aminoAcidAlt: string; aminoAcidRef: string; aminoAcids: string; codonChange: string; consequenceTerms: string; entrezGeneId: string; exon: string; hgvsc: string; hgvsp: string; hgvspShort: string; ... 4 more ...; variantClassification: string; }' is missing the following properties from type 'TranscriptConsequenceSummary': 'polyphenPrediction', 'polyphenScore', 'siftPrediction', 'siftScore'

but local is fine

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leexgh commented Oct 14, 2020

This is a testing version, it has a lot of things could be cleaned up or updated. We can update it later

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Looks good, let's make sure that it works in Signal

packages/react-variant-view/package.json Outdated Show resolved Hide resolved
Comment on lines +4 to +6
// TODO customize domain?
export const genomeNexusDomain = 'https://www.genomenexus.org/';
const genomeNexusInternalClient = new GenomeNexusAPI(genomeNexusDomain);
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Right, most likely we would like to customize this. How do we do the genome nexus client customization for react-mutation-mapper? Is it possible to do it the same way?

import { VariantAnnotationSummary } from 'genome-nexus-ts-api-client';
import { getTranscriptConsequenceSummary } from './AnnotationSummaryUtil';

export function variantToMutation(
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We may want to move some of these utility functions into cbioportal-utils, but I guess it is okay to leave them here at this point.

"react": "^15.0.0 || ^16.0.0",
"react-dom": "^15.0.0 || ^16.0.0"
},
"dependencies": {
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We need to make sure that these dependencies are complete. This package may still work inside the monorepo even if some dependencies are not listed here. But when we include the package in another project we may get missing dependency errors. For now we can test it with signal to see if it works fine (after publishing the beta version to npm).

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leexgh commented Oct 16, 2020

Update ideas:

  1. Do we like the styles? (not located in the center without mutation mapper)
  2. Click gene to go to gene page
  3. Some warning needs to be fixed

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leexgh commented Oct 22, 2020

@onursumer Thank you! I've updated the version and no more complain about it

@leexgh leexgh requested a review from onursumer October 22, 2020 17:48
@inodb inodb added the cl-package Improvements related to a package label Oct 23, 2020
@inodb inodb merged commit 8bc9c60 into cBioPortal:master Oct 23, 2020
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