Add OncoKB MSI-H, TMB-H annotation #3469
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| <p>{this.props.geneSummary}</p> | ||
| <p>{this.props.variantSummary}</p> | ||
| {this.props.usingPublicOncoKbInstance ? ( | ||
| <p className={mainStyles.disclaimer}> | ||
| Therapeutic levels are not available in this instance of | ||
| cBioPortal.{' '} | ||
| <DefaultTooltip | ||
| overlayStyle={{ | ||
| maxWidth: 400, | ||
| }} | ||
| overlay={publicInstanceDisclaimerOverLay} | ||
| > | ||
| <i className={'fa fa-info-circle'}></i> | ||
| </DefaultTooltip> | ||
| </p> | ||
| ) : ( | ||
| <> | ||
| <p>{this.props.tumorTypeSummary}</p> | ||
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| {this.props.treatments!.length > 0 && ( | ||
| <div | ||
| style={{ | ||
| marginTop: 10, | ||
| }} | ||
| > | ||
| <OncoKbTreatmentTable | ||
| variant={this.props.variant || ''} | ||
| pmidData={this.props.pmidData!} | ||
| treatments={this.props.treatments!} | ||
| /> | ||
| </div> | ||
| )} | ||
| </> | ||
| )} | ||
| </> |
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No need to review, just moved out of the tabs context below.
| MSI_H, | ||
| OTHER_BIOMARKER_HUGO_SYMBOL, | ||
| TMB_H, | ||
| } from 'react-mutation-mapper/src/component/oncokb/constants'; |
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Direct import from package src directory is likely to cause a lot of issues. Let's export these constants and do this instead:
| } from 'react-mutation-mapper/src/component/oncokb/constants'; | |
| } from 'react-mutation-mapper'; |
We can also consider moving these constants into cbioportal-utils if you think it is a better package for them.
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Not yet, let's keep it under RMM for now.
| @@ -658,6 +679,87 @@ export default class PatientViewPage extends React.Component< | |||
| uniqueSampleKey={sample.id} | |||
| /> | |||
| )} | |||
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| {this.patientViewPageStore | |||
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Contents of these two spans and the render conditions are pretty similar to each other, it might be better to have a small customizable functional component for it.
| MSI_H, | ||
| OTHER_BIOMARKER_HUGO_SYMBOL, | ||
| TMB_H, | ||
| } from 'react-mutation-mapper/src/component/oncokb/constants'; |
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(See the previous related comment)
| } from 'react-mutation-mapper/src/component/oncokb/constants'; | |
| } from 'react-mutation-mapper'; |
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| @computed get otherBiomarkerQueries() { | ||
| const queries: AnnotateMutationByProteinChangeQuery[] = []; | ||
| if (_.keys(this.sampleMsiHInfo).length > 0) { |
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The if blocks are almost identical, may be worth combining them.
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Yeah, previously I don't like to add too many key value pairs for these. But since I'm gonna combine the logic in the PatientViewPage anyway, I will update here too.
src/shared/lib/StoreUtils.ts
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| ); | ||
| } | ||
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| export function getNumberClinicalDataValue( |
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Should we use numerical instead of number in the function name?
| export function getNumberClinicalDataValue( | |
| export function getNumericalClinicalDataValue( |
src/shared/lib/StoreUtils.ts
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| } | ||
| } | ||
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| export function getSampleNumberClinicalDataValue( |
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Same as above. numerical instead of number?
| export function getSampleNumberClinicalDataValue( | |
| export function getSampleNumericalClinicalDataValue( |
| [sampleId: string]: { [queryType: string]: IndicatorQueryResp }; | ||
| }>({ | ||
| invoke: async () => { | ||
| const allResult = await oncokbClient.annotateMutationsByProteinChangePostUsingPOST_1( |
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Yeah, the oncokb has two sets of apis and they sharing the same name. The swagger generates as POST_1.
| }; | ||
| }); | ||
| const map = _.chain(updatedResult) | ||
| .groupBy('sampleId') |
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string shortcut not typesafe
| }); | ||
| const map = _.chain(updatedResult) | ||
| .groupBy('sampleId') | ||
| .mapValues(group => _.keyBy(group, 'type')) |
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again not string shortcuts
| export function getNumericalClinicalDataValue( | ||
| clinicalData: ClinicalData | ||
| ): number | undefined { | ||
| if (Number.isNaN(clinicalData.value)) { |
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Just checking but this assumes that clinicalData.value is numerical (if in string form). Number.isNaN("blah") is false so you could get Number("blah") which would be NaN.
Do not show subtitle when hugoSymbol is Other Biomarker Signed-off-by: Hongxin Zhang <hongxin@cbio.mskcc.org>
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The failing tests are irrelevant to this pr. |
The following annotations will be added when sample has TMB, MSI scores.
The thresholds for both score are >=10.
Patient View Header
MSI-H Annotation
TMB-H Annotation
Fix cBioPortal/cbioportal#6862