-
- Mutation Assessor
- {' '}
- predicts the functional impact of amino-acid substitutions in
- proteins, such as mutations discovered in cancer or missense
- polymorphisms. The functional impact is assessed based on
- evolutionary conservation of the affected amino acid in protein
- homologs. The method has been validated on a large set (60k) of
- disease associated (OMIM) and polymorphic variants.
+
{(maData.functionalImpactScore ||
@@ -245,86 +216,12 @@ export default class MutationAssessor extends React.Component<
)}
-
- Please refer to the score range{' '}
-
- here
-
- .
-
) : null;
- const xVar =
- xVarLink &&
- maData.uniprotId.length !== 0 &&
- maData.variant.length !== 0 ? (
-
- ) : null;
-
- const msa =
- msaLink && maData.msaLink.length !== 0 ? (
-
- ) : null;
-
- const pdb =
- pdbLink && maData.pdbLink.length !== 0 ? (
-
- ) : null;
-
return (
- WARNING:
- All URLs in this website are private - do NOT include
- in manuscripts.
+ Attention:
+ Please read and follow the{' '}
+
+ rules about usage of MSK clinical sequencing data in
+ manuscripts
+
+ .
}
+ dismissButtonText={'Acknowledge'}
persistenceKey={STUDY_VIEW_WARNING_PERSISTENCE_KEY}
expirationInDays={90}
clauses={[
@@ -56,31 +66,13 @@ export const StudyAgreement: React.FunctionComponent<{}> = function({}) {
public cBioPortal.
,
<>
- When adding a link to a cBioPortal cohort in a manuscript,{' '}
-
- I will not link to this private portal (
- {window.location.hostname})
-
- , but will instead link to this study on the public
- cBioPortal (
-
- cbioportal.org
-
- ). Contact{' '}
-
- cbioportal@cbio.mskcc.org
- {' '}
- with any questions about getting the data transferred to the
- public cBioPortal.
- ,
- <>
- I have read the{' '}
+ I have read and agree to the{' '}
- MSK-IMPACT Data publication guidelines (intranet/VPN
- only)
+ MSK-IMPACT Memorial Hospital Research Data Governance
+ publication guidelines
.
,
diff --git a/src/globalStyles/global.scss b/src/globalStyles/global.scss
index 81f33b14a2d..7b1839b6d60 100755
--- a/src/globalStyles/global.scss
+++ b/src/globalStyles/global.scss
@@ -47,6 +47,14 @@ div:active {
}
}
+.form-group-inline {
+ @extend .form-group;
+
+ label {
+ margin-right: 6px;
+ }
+}
+
.posRelative {
position: relative;
}
diff --git a/src/pages/patientView/patientHeader/SignificantMutationalSignatures.tsx b/src/pages/patientView/patientHeader/SignificantMutationalSignatures.tsx
index c62f011fc15..da59e06fd5b 100644
--- a/src/pages/patientView/patientHeader/SignificantMutationalSignatures.tsx
+++ b/src/pages/patientView/patientHeader/SignificantMutationalSignatures.tsx
@@ -74,11 +74,13 @@ export default class SignificantMutationalSignatures extends React.Component<
)}
{_.map(dataToShow, significantSignature => (
@@ -89,13 +91,14 @@ export default class SignificantMutationalSignatures extends React.Component<
{dataToShow.map(significantSignature => (
- {significantSignature.meta.name}
+ {significantSignature.meta?.name || 'NA'}
@@ -113,7 +116,7 @@ export default class SignificantMutationalSignatures extends React.Component<
significantMutationalSignaturesForSample,
(acc, significantSignature) => {
const color = getColorByMutationalSignatureCategory(
- significantSignature.meta.category
+ significantSignature.meta?.category
);
if (color in acc) {
acc[color] += significantSignature.value;
diff --git a/src/pages/resultsView/ResultsViewPage.tsx b/src/pages/resultsView/ResultsViewPage.tsx
index 09423eeade7..62a0868d13a 100644
--- a/src/pages/resultsView/ResultsViewPage.tsx
+++ b/src/pages/resultsView/ResultsViewPage.tsx
@@ -265,7 +265,10 @@ export default class ResultsViewPage extends React.Component<
entrezGeneIdToGene={store.entrezGeneIdToGene}
sampleKeyToSample={store.sampleKeyToSample}
genes={store.genes}
- clinicalAttributes={store.clinicalAttributes}
+ clinicalAttributes={
+ store.plotClinicalAttributes
+ }
+ customAttributes={store.customAttributes}
genesets={store.genesets}
genericAssayEntitiesGroupByMolecularProfileId={
store.genericAssayEntitiesGroupByMolecularProfileId
diff --git a/src/pages/resultsView/ResultsViewPageStore.ts b/src/pages/resultsView/ResultsViewPageStore.ts
index ea50031be8e..adef8acb186 100644
--- a/src/pages/resultsView/ResultsViewPageStore.ts
+++ b/src/pages/resultsView/ResultsViewPageStore.ts
@@ -1093,7 +1093,7 @@ export class ResultsViewPageStore extends AnalysisStore
this.studyIds,
this.clinicalAttributes_profiledIn,
this.clinicalAttributes_comparisonGroupMembership,
- this.clinicalAttributes_customCharts,
+ this.customAttributes,
this.samples,
this.patients,
],
@@ -1142,7 +1142,7 @@ export class ResultsViewPageStore extends AnalysisStore
...specialAttributes,
...this.clinicalAttributes_profiledIn.result!,
...this.clinicalAttributes_comparisonGroupMembership.result!,
- ...this.clinicalAttributes_customCharts.result!,
+ ...this.customAttributes.result!,
];
},
});
@@ -1187,7 +1187,7 @@ export class ResultsViewPageStore extends AnalysisStore
this.studyToDataQueryFilter,
this.clinicalAttributes_profiledIn,
this.clinicalAttributes_comparisonGroupMembership,
- this.clinicalAttributes_customCharts,
+ this.customAttributes,
],
invoke: async () => {
let clinicalAttributeCountFilter: ClinicalAttributeCountFilter;
@@ -1270,7 +1270,7 @@ export class ResultsViewPageStore extends AnalysisStore
);
}
// add counts for custom chart clinical attributes
- for (const attr of this.clinicalAttributes_customCharts.result!) {
+ for (const attr of this.customAttributes.result!) {
ret[attr.clinicalAttributeId] = attr.data!.filter(
d => d.value !== 'NA'
).length;
@@ -2723,7 +2723,17 @@ export class ResultsViewPageStore extends AnalysisStore
default: [],
});
- readonly clinicalAttributes_customCharts = remoteData({
+ readonly plotClinicalAttributes = remoteData({
+ await: () => [this.clinicalAttributes, this.customAttributes],
+ invoke: async () => {
+ return _.filter(
+ this.clinicalAttributes.result!,
+ attr => !this.customAttributes.result!.includes(attr)
+ );
+ },
+ });
+
+ readonly customAttributes = remoteData({
await: () => [this.sampleMap],
invoke: async () => {
let ret: ExtendedClinicalAttribute[] = [];
@@ -5693,7 +5703,7 @@ export class ResultsViewPageStore extends AnalysisStore
this.coverageInformation,
this.filteredSampleKeyToSample,
this.filteredPatientKeyToPatient,
- this.clinicalAttributes_customCharts
+ this.customAttributes
);
public mutationCache = new MobxPromiseCache<
diff --git a/src/pages/resultsView/mutation/Mutations.tsx b/src/pages/resultsView/mutation/Mutations.tsx
index 9c098d005ff..24866e63a36 100644
--- a/src/pages/resultsView/mutation/Mutations.tsx
+++ b/src/pages/resultsView/mutation/Mutations.tsx
@@ -334,14 +334,20 @@ export default class Mutations extends React.Component<
count: number,
mutations: Mutation[],
axisMode: AxisScale
- ): JSX.Element {
- return (
- {
await: () => [
this.props.store.clinicalAttributes,
this.clinicalAttributeIdToAvailableFrequency,
- this.props.store.clinicalAttributes_customCharts,
+ this.props.store.customAttributes,
],
invoke: () => {
const uniqueAttributes = _.uniqBy(
@@ -167,7 +167,7 @@ export default class TracksMenu extends React.Component {
};
const customChartClinicalAttributeIds = _.keyBy(
- this.props.store.clinicalAttributes_customCharts.result!,
+ this.props.store.customAttributes.result!,
a => a.clinicalAttributeId
);
diff --git a/src/pages/studyView/StudyViewPage.tsx b/src/pages/studyView/StudyViewPage.tsx
index 0971f3c73fe..5628f49ba2d 100644
--- a/src/pages/studyView/StudyViewPage.tsx
+++ b/src/pages/studyView/StudyViewPage.tsx
@@ -769,6 +769,9 @@ export default class StudyViewPage extends React.Component<
clinicalAttributes={
this.store.clinicalAttributes
}
+ customAttributes={
+ this.store.customAttributes
+ }
genesets={this.store.genesets}
genericAssayEntitiesGroupByMolecularProfileId={
this.store
diff --git a/src/pages/studyView/StudyViewPageStore.ts b/src/pages/studyView/StudyViewPageStore.ts
index cafc79680de..faf5c3cc105 100644
--- a/src/pages/studyView/StudyViewPageStore.ts
+++ b/src/pages/studyView/StudyViewPageStore.ts
@@ -11477,7 +11477,7 @@ export class StudyViewPageStore
),
});
- readonly clinicalAttributes_customCharts = remoteData({
+ readonly customAttributes = remoteData({
await: () => [this.sampleMap],
invoke: async () => {
let ret: ExtendedClinicalAttribute[] = [];
@@ -11523,7 +11523,7 @@ export class StudyViewPageStore
this.coverageInformation,
this.filteredSampleKeyToSample,
this.filteredPatientKeyToPatient,
- this.clinicalAttributes_customCharts
+ this.customAttributes
);
private _numericGeneMolecularDataCache = new MobxPromiseCache<
diff --git a/src/pages/studyView/StudyViewUtils.tsx b/src/pages/studyView/StudyViewUtils.tsx
index e2e8b78bc78..06c56f02131 100644
--- a/src/pages/studyView/StudyViewUtils.tsx
+++ b/src/pages/studyView/StudyViewUtils.tsx
@@ -903,7 +903,8 @@ export function getVirtualStudyDescription(
attributeNamesSet: { [id: string]: string },
molecularProfileNameSet: { [id: string]: string },
caseListNameSet: { [key: string]: string },
- user?: string
+ user?: string,
+ hideSampleCounts: boolean = false
) {
let descriptionLines: string[] = [];
const createdOnStr = 'Created on';
@@ -917,18 +918,24 @@ export function getVirtualStudyDescription(
_.flatMap(studyWithSamples, study => study.uniqueSampleKeys)
);
descriptionLines.push(
- `${uniqueSampleKeys.length} sample${
- uniqueSampleKeys.length > 1 ? 's' : ''
- } from ${studyWithSamples.length} ${
- studyWithSamples.length > 1 ? 'studies:' : 'study:'
- }`
+ (hideSampleCounts
+ ? 'Samples'
+ : `${uniqueSampleKeys.length} sample${
+ uniqueSampleKeys.length > 1 ? 's' : ''
+ }`) +
+ ` from ${studyWithSamples.length} ${
+ studyWithSamples.length > 1 ? 'studies:' : 'study:'
+ }`
);
//add individual studies sample count
studyWithSamples.forEach(studyObj => {
descriptionLines.push(
- `- ${studyObj.name} (${
- studyObj.uniqueSampleKeys.length
- } sample${uniqueSampleKeys.length > 1 ? 's' : ''})`
+ `- ${studyObj.name}` +
+ (hideSampleCounts
+ ? ''
+ : ` (${studyObj.uniqueSampleKeys.length} sample${
+ uniqueSampleKeys.length > 1 ? 's' : ''
+ })`)
);
});
//add filters
diff --git a/src/pages/studyView/addChartButton/AddChartButton.tsx b/src/pages/studyView/addChartButton/AddChartButton.tsx
index 8246b346ba2..0955e19b9fd 100644
--- a/src/pages/studyView/addChartButton/AddChartButton.tsx
+++ b/src/pages/studyView/addChartButton/AddChartButton.tsx
@@ -19,7 +19,11 @@ import { StudyViewPageTabKeyEnum } from 'pages/studyView/StudyViewPageTabs';
import autobind from 'autobind-decorator';
import _ from 'lodash';
import AddChartByType from './addChartByType/AddChartByType';
-import { DefaultTooltip, remoteData } from 'cbioportal-frontend-commons';
+import {
+ DefaultTooltip,
+ isWebdriver,
+ remoteData,
+} from 'cbioportal-frontend-commons';
import CustomCaseSelection from './customCaseSelection/CustomCaseSelection';
import {
calculateClinicalDataCountFrequency,
@@ -50,6 +54,7 @@ import { CustomChartData } from 'shared/api/session-service/sessionServiceModels
import ReactSelect from 'react-select';
import { GenericAssayMeta } from 'cbioportal-ts-api-client';
import { DataTypeConstants } from 'shared/constants';
+import { Else, If, Then } from 'react-if';
export interface IAddChartTabsProps {
store: StudyViewPageStore;
@@ -629,6 +634,23 @@ class AddChartTabs extends React.Component {
@computed get notificationMessages() {
let notificationMessages: JSX.Element[] = [];
+ if (!this.props.store.isLoggedIn) {
+ notificationMessages.push(
+ <>
+
+ to add custom data charts to your profile.
+
+ );
+ return notificationMessages;
+ }
+
if (this.props.store.customChartSet.size > 0) {
// Notify if there any shared custom data
if (this.existSharedCustomData) {
@@ -644,28 +666,6 @@ class AddChartTabs extends React.Component {
are shared custom data.
);
- }
- // Notify that shared and page-session custom data are not saved for non-logged users
- if (
- !this.props.store.isLoggedIn &&
- this.props.store.appStore.isSocialAuthenticated
- ) {
- if (notificationMessages.length > 0) {
- notificationMessages.push(
); - } - notificationMessages.push( - <> - - to save custom data charts to your profile. - - ); } else if (this.existSharedCustomData) { // Notify if shared custom data are saved to user profile if (notificationMessages.length > 0) { @@ -911,104 +911,135 @@ class AddChartTabs extends React.Component {
this.getTabsWidth - CONTAINER_PADDING_WIDTH,
}}
>
- {this.customChartDataOptions.length > 0 && (
-
+ {!this.props.store.isLoggedIn && (
+ <>
+
+ + Please {this.notificationMessages} + + )} - - {this.isAddNewChartWindowVisible && ( - {
- this.showAddNewChart = false;
- this.savingCustomData = true;
- this.updateInfoMessage(
- `Saving ${chart.displayName}`
- );
- this.props.store
- .addCustomChart(chart)
- .then(() => {
- this.savingCustomData = false;
- this.updateInfoMessage(
- `${chart.displayName} has been added.`
- );
- });
- }}
- />
- )}
-
- <>
- {this.customChartDataOptions.length > 0 && (
- <>
-
-
+ {this.customChartDataOptions.length > 0 && (
+
+ )}
+
+ {this.isAddNewChartWindowVisible && (
+ {
- this.props.store.toggleCustomChartMarkedForDeletion(
- id
- );
- }}
- restoreChart={(id: string) => {
- this.props.store.toggleCustomChartMarkedForDeletion(
- id
- );
- }}
- markedForDeletion={
+ submitButtonText={'Add Chart'}
+ queriedStudies={
this.props.store
- .customChartGroupMarkedForDeletion
+ .queriedPhysicalStudyIds
+ .result
}
+ isChartNameValid={
+ this.props.store
+ .isChartNameValid
+ }
+ getDefaultChartName={
+ this.props.store
+ .getDefaultCustomChartName
+ }
+ disableSubmitButton={
+ this.savingCustomData
+ }
+ onSubmit={(
+ chart: CustomChartData
+ ) => {
+ this.showAddNewChart = false;
+ this.savingCustomData = true;
+ this.updateInfoMessage(
+ `Saving ${chart.displayName}`
+ );
+ this.props.store
+ .addCustomChart(chart)
+ .then(() => {
+ this.savingCustomData = false;
+ this.updateInfoMessage(
+ `${chart.displayName} has been added.`
+ );
+ });
+ }}
/>
-
- )}
- {this.notificationMessages.length > 0 && (
+ )}
+
<>
-
- - Note: {this.notificationMessages} - + {this.customChartDataOptions.length > + 0 && ( + <> +
+ {
+ this.props.store.toggleCustomChartMarkedForDeletion(
+ id
+ );
+ }}
+ restoreChart={(
+ id: string
+ ) => {
+ this.props.store.toggleCustomChartMarkedForDeletion(
+ id
+ );
+ }}
+ markedForDeletion={
+ this.props.store
+ .customChartGroupMarkedForDeletion
+ }
+ />
+
+ )}
+ {this.notificationMessages.length >
+ 0 && (
+ <>
+
+ + Note:{' '} + {this.notificationMessages} + + + )} - )} - + + )}
+ internalClient.getAllStudyResourceDataInStudyPatientSampleUsingGET({
+ studyId: studyId,
+ projection: 'DETAILED',
+ })
+ );
+
+ return Promise.all(allResources).then(allResources =>
+ _(allResources)
+ .flatMap()
+ .value()
+ );
+}
+
function getResourceDataOfPatients(studyClinicalData: {
[uniqueSampleKey: string]: ClinicalData[];
}) {
@@ -86,6 +102,7 @@ function buildItemsAndResources(resourceData: {
typeOfResource: resource?.resourceDefinition?.displayName,
description: resource?.resourceDefinition?.description,
url: resource?.url,
+ resourceId: resource?.resourceId,
}))
)
.value();
@@ -95,28 +112,35 @@ function buildItemsAndResources(resourceData: {
async function fetchFilesLinksData(
filters: StudyViewFilter,
- sampleIdResourceData: { [sampleId: string]: ResourceData[] },
+ selectedSamples: Array,
searchTerm: string | undefined,
sortAttributeId: string | undefined,
sortDirection: 'asc' | 'desc' | undefined,
recordLimit: number
) {
- const studyClinicalDataResponse = await getAllClinicalDataByStudyViewFilter(
- filters,
- searchTerm,
- sortAttributeId,
- sortDirection,
- recordLimit,
- 0
- );
+ const selectedStudyIds = [
+ ...new Set(selectedSamples.map(item => item.studyId)),
+ ];
+
+ // sampleIds (+patientIds) for the selectedSamples
+ const selectedIds = new Map([
+ ...selectedSamples.map(item => [item.sampleId, item.studyId] as const),
+ ...selectedSamples.map(item => [item.patientId, item.studyId] as const),
+ ]);
- const resourcesForPatients = await getResourceDataOfPatients(
- studyClinicalDataResponse.data
+ // Fetch resources for entire study
+ const resourcesForEntireStudy = await getResourceDataOfEntireStudy(
+ selectedStudyIds
);
- const resourcesForPatientsAndSamples: { [key: string]: ResourceData[] } = {
- ...sampleIdResourceData,
- ...resourcesForPatients,
- };
+
+ // Filter the resources to consist of only studyView selected samples
+ // Also keep patient level resources (e.g. Those don't have a sampleId)
+ const resourcesForPatientsAndSamples = _(resourcesForEntireStudy)
+ .filter(resource =>
+ selectedIds.has(resource.sampleId || resource.patientId)
+ )
+ .groupBy(r => r.patientId)
+ .value();
// we create objects with the necessary properties for each resource
// calculate the total number of resources per patient.
@@ -195,7 +219,6 @@ export class FilesAndLinks extends React.Component {
await: () => [
this.props.store.selectedSamples,
this.props.store.resourceDefinitions,
- this.props.store.sampleResourceData,
],
onError: () => {},
invoke: async () => {
@@ -205,12 +228,13 @@ export class FilesAndLinks extends React.Component {
const resources = await fetchFilesLinksData(
this.props.store.filters,
- this.props.store.sampleResourceData.result!,
+ this.props.store.selectedSamples.result,
this.searchTerm,
'patientId',
'asc',
RECORD_LIMIT
);
+
return Promise.resolve(resources);
},
});
@@ -259,18 +283,41 @@ export class FilesAndLinks extends React.Component {
'Type Of Resource'
),
render: (data: { [id: string]: string }) => {
+ const path = `patient/openResource_${data.resourceId}`;
return (
+ );
+ },
+ },
+
+ {
+ ...this.getDefaultColumnConfig('resourceUrl', ''),
+ render: (data: { [id: string]: string }) => {
+ return (
+
);
@@ -287,7 +334,7 @@ export class FilesAndLinks extends React.Component {
{
...this.getDefaultColumnConfig(
'resourcesPerPatient',
- 'Number of Resource Per Patient',
+ 'Resources per Patient',
true
),
render: (data: { [id: string]: number }) => {
diff --git a/src/pages/studyView/virtualStudy/VirtualStudy.tsx b/src/pages/studyView/virtualStudy/VirtualStudy.tsx
index 4a492d847c4..f55a3db3404 100644
--- a/src/pages/studyView/virtualStudy/VirtualStudy.tsx
+++ b/src/pages/studyView/virtualStudy/VirtualStudy.tsx
@@ -97,7 +97,8 @@ export default class VirtualStudy extends React.Component<
{}
> {
@observable.ref private name: string;
- @observable.ref private description: string;
+ @observable.ref private customDescription: string | undefined;
+ @observable.ref private dynamic: boolean = false;
@observable private saving = false;
@observable private sharing = false;
@@ -107,17 +108,6 @@ export default class VirtualStudy extends React.Component<
super(props);
makeObservable(this);
this.name = props.name || '';
- this.description =
- props.description ||
- getVirtualStudyDescription(
- this.props.description,
- this.props.studyWithSamples,
- this.props.filter,
- this.attributeNamesSet,
- this.props.molecularProfileNameSet,
- this.props.caseListNameSet,
- this.props.user
- );
}
@computed get namePlaceHolder() {
@@ -167,6 +157,7 @@ export default class VirtualStudy extends React.Component<
study => study.studyId
),
studies: studies,
+ dynamic: this.dynamic,
};
return await sessionServiceClient.saveVirtualStudy(
parameters,
@@ -231,6 +222,30 @@ export default class VirtualStudy extends React.Component<
);
}
+ getDefuaultDescriptionByType(dynamic: boolean) {
+ return getVirtualStudyDescription(
+ this.props.description,
+ this.props.studyWithSamples,
+ this.props.filter,
+ this.attributeNamesSet,
+ this.props.molecularProfileNameSet,
+ this.props.caseListNameSet,
+ this.props.user,
+ dynamic
+ );
+ }
+
+ @computed get description() {
+ const noCustomDescriptionProvided =
+ this.customDescription == undefined ||
+ this.customDescription ===
+ this.getDefuaultDescriptionByType(!this.dynamic);
+ if (noCustomDescriptionProvided) {
+ return this.getDefuaultDescriptionByType(this.dynamic);
+ }
+ return this.customDescription || '';
+ }
+
render() {
return (
+ Mutation Assessor predicts the functional impact of amino-acid
+ substitutions in proteins, such as mutations discovered in
+ cancer or missense polymorphisms. The functional impact is
+ assessed based on evolutionary conservation of the affected
+ amino acid in protein homologs. The method has been validated on
+ a large set of disease associated and polymorphic variants (
+
+ ClinVar
+
+ ).
+
+ + Mutation Assessor V4 data is available in the portal since + Oct. 8, 2024. + {' '} + New manuscript is in progress. Click{` `} + + here + + {` `} to see information about V3 data.
);
}
@@ -143,24 +151,6 @@ export default class MutationAssessor extends React.Component<
);
}
- // This is mostly to make the legacy MA links work
- private static maLink(link: string | undefined) {
- let url = null;
-
- // ignore invalid links ("", "NA", "Not Available")
- if (link) {
- // getma.org is the legacy link, need to replace it with the actual value
- url = link.replace('getma.org', 'mutationassessor.org/r3');
-
- // prepend "http://" if needed
- if (url.indexOf('http://') !== 0) {
- url = `http://${url}`;
- }
- }
-
- return url;
- }
-
constructor(props: IMutationAssessorProps) {
super(props);
@@ -169,21 +159,13 @@ export default class MutationAssessor extends React.Component<
public render() {
let maContent: JSX.Element = ;
- const dataSource = (
- <>
- Mutation Assessor
-
- {!this.props.isCanonicalTranscriptSelected && *}
-
- );
-
if (
this.props.mutationAssessor &&
- this.props.mutationAssessor.functionalImpact != null &&
- this.props.mutationAssessor.functionalImpact !== ''
+ this.props.mutationAssessor.functionalImpactPrediction != null &&
+ this.props.mutationAssessor.functionalImpactPrediction !== ''
) {
const maData = this.props.mutationAssessor;
- maContent = {maData.functionalImpact};
+ maContent = {maData.functionalImpactPrediction};
} else {
maContent = N/A;
}
@@ -192,25 +174,19 @@ export default class MutationAssessor extends React.Component<
+ + Mutation Assessor V4 data is available in the portal since + Oct. 8, 2024. + {' '} + New manuscript is in progress. Click{` `} + + here + + {` `} to see information about V3 data.
{this.mutationAssessorTooltip(
-
- {dataSource}
-
+ <>
+ Mutation Assessor
+
+ {!this.props.isCanonicalTranscriptSelected && (
+ *
+ )}
+
)}
{this.mutationAssessorTooltip(
-
- {maContent}
-
+ {maContent}
)}
@@ -221,12 +197,7 @@ export default class MutationAssessor extends React.Component<
private mutationAssessorData() {
if (this.props.mutationAssessor) {
const maData = this.props.mutationAssessor;
- const xVarLink = MutationAssessor.maLink(
- `http://mutationassessor.org/r3/?cm=var&p=${maData.uniprotId}&var=${maData.variant}`
- );
- const msaLink = MutationAssessor.maLink(maData.msaLink);
- const pdbLink = MutationAssessor.maLink(maData.pdbLink);
- const impact = maData.functionalImpact ? (
+ const impact = maData.functionalImpactPrediction ? (
{impact}
- {msa}
- {pdb}
- {xVar}
);
diff --git a/src/appBootstrapper.tsx b/src/appBootstrapper.tsx
index d36088736a4..33dc126fd0a 100755
--- a/src/appBootstrapper.tsx
+++ b/src/appBootstrapper.tsx
@@ -1,6 +1,6 @@
import React from 'react';
import ReactDOM from 'react-dom';
-import { configure } from 'mobx';
+import { configure, toJS } from 'mobx';
import { Provider } from 'mobx-react';
import { Router } from 'react-router-dom';
import { createBrowserHistory } from 'history';
@@ -27,7 +27,12 @@ import browser from 'bowser';
import { setNetworkListener } from './shared/lib/ajaxQuiet';
import { initializeTracking, sendToLoggly } from 'shared/lib/tracking';
import superagentCache from 'superagent-cache';
-import { getBrowserWindow, onMobxPromise } from 'cbioportal-frontend-commons';
+import {
+ getBrowserWindow,
+ hashString,
+ isWebdriver,
+ onMobxPromise,
+} from 'cbioportal-frontend-commons';
import { AppStore } from './AppStore';
import { handleLongUrls } from 'shared/lib/handleLongUrls';
import 'shared/polyfill/canvasToBlob';
@@ -39,6 +44,7 @@ import { FeatureFlagStore } from 'shared/FeatureFlagStore';
import eventBus from 'shared/events/eventBus';
import { SiteError } from 'shared/model/appMisc';
import load from 'little-loader';
+import internalClient from 'shared/api/cbioportalInternalClientInstance';
export interface ICBioWindow {
globalStores: {
@@ -206,6 +212,69 @@ superagent.Request.prototype.end = function(callback) {
}
});
};
+
+function enableDataDogTracking(store: AppStore) {
+ datadogLogs.init({
+ clientToken: 'pub9a94ebb002f105ff44d8e427b6549775',
+ site: 'datadoghq.com',
+ service: 'cbioportalinternal',
+ forwardErrorsToLogs: true,
+ sessionSampleRate: 100,
+ } as any);
+
+ const match = [
+ /filtered-samples/,
+ /clinical-data-bin-counts/,
+ /generic-assay-data-bin-counts/,
+ /mutated-genes/,
+ /molecular-profile-sample-counts/,
+ /cna-genes/,
+ /structuralvariant-genes/,
+ /clinical-data-counts/,
+ /sample-lists-counts/,
+ /clinical-data-density-plot/,
+ /clinical-data-violin-plots/,
+ /genomic-data-counts/,
+ /mutation-data-counts/,
+ /clinical-event-type-counts/,
+ /treatments\/patient-counts/,
+ /treatments\/sample-counts/,
+ /genomic-data-bin-counts/,
+ /clinical-event-type-counts/,
+ ];
+
+ const oldRequest = (internalClient as any).request;
+ (internalClient as any).request = function(...args: any) {
+ try {
+ let url = args[1];
+
+ if (Object.keys(args[4]).length) {
+ url = url + '?' + $.param(args[4]);
+ }
+
+ const data = args[2];
+
+ const studyIds = data.studyIds || data.studyViewFilter.studyIds;
+
+ const appName = store.serverConfig.app_name;
+
+ if (studyIds.length < 4 && _.some(match, re => re.test(url))) {
+ const hash = hashString(url + JSON.stringify(toJS(data)));
+ datadogLogs.logger.info('study view request', {
+ url,
+ data,
+ hash,
+ appName,
+ });
+ }
+ } catch (ex) {
+ // fail silently
+ }
+
+ return oldRequest.apply(this, args);
+ };
+}
+
//
browserWindow.routingStore = routingStore;
@@ -236,24 +305,6 @@ let render = (key?: number) => {
]`;
}
- if (stores.appStore.serverConfig.app_name === 'mskcc-portal') {
- datadogLogs.init({
- clientToken: 'pub9a94ebb002f105ff44d8e427b6549775',
- site: 'datadoghq.com',
- service: 'cbioportalinternal',
- forwardErrorsToLogs: true,
- sessionSampleRate: 100,
- beforeSend: (log: any) => {
- switch (log.origin) {
- case 'console':
- return false;
- default:
- // let dd send log
- }
- },
- } as any);
- }
-
const rootNode = document.getElementById('reactRoot');
ReactDOM.render(
@@ -319,6 +370,15 @@ $(document).ready(async () => {
initializeAppStore(stores.appStore);
+ if (
+ ['genie-public-portal', 'public-portal'].includes(
+ stores.appStore.serverConfig.app_name!
+ ) &&
+ !isWebdriver()
+ ) {
+ enableDataDogTracking(stores.appStore);
+ }
+
await loadCustomJs();
render();
diff --git a/src/appShell/App/usageAgreements/StudyAgreement.tsx b/src/appShell/App/usageAgreements/StudyAgreement.tsx
index f430ba59921..75ba1fcc0ec 100644
--- a/src/appShell/App/usageAgreements/StudyAgreement.tsx
+++ b/src/appShell/App/usageAgreements/StudyAgreement.tsx
@@ -28,11 +28,21 @@ export const StudyAgreement: React.FunctionComponent<{}> = function({}) {
-
- {significantSignature.meta.name}
+
+ {significantSignature.meta?.name || 'NA'}
:
- {significantSignature.meta.description}
+
+ {significantSignature.meta?.description || 'NA'}
+
))}
); - } - notificationMessages.push( - <> - - to save custom data charts to your profile. - - ); } else if (this.existSharedCustomData) { // Notify if shared custom data are saved to user profile if (notificationMessages.length > 0) { @@ -911,104 +911,135 @@ class AddChartTabs extends React.Component
+ + Please {this.notificationMessages} + + )} - - {this.isAddNewChartWindowVisible && ( -
-
- - Note: {this.notificationMessages} - + {this.customChartDataOptions.length > + 0 && ( + <> +
+
+ + Note:{' '} + {this.notificationMessages} + + + )} - )} - + + )}
- (this.description =
+ (this.customDescription =
event.currentTarget.value)
}
/>
+
+
+
+
+
+
+ }
+ >
+ + + Type of Virtual + Study: + +
++ This Virtual Study + will contain the set + of sample IDs + currently selected. + Furthermore, you can + define this Virtual + Study to be either + static or dynamic: +
+-
+
- + + Static + {' '} + – Sample IDs are + the ones + currently + selected and no + new samples are + added to this + Virtual Study + set, even if the + database gets + updated with new + samples that + match the same + filtering/selection + criteria as the + samples in the + current set. + +
- + + Dynamic + {' '} + – Unlike the + Static option, + any new samples + added to the + database that + match the + criteria of this + Virtual Study + will + automatically be + included in its + sample set. + +
{this.showSaveButton && (
@@ -122,7 +122,7 @@ export default class UsageAgreement extends React.Component<
container={this}
aria-labelledby="contained-modal-title"
>
-
+
= ({
+ alphaMissensePrediction,
+ alphaMissenseScore,
+}) => {
+ const tooltipContent = () => {
+ const impact = alphaMissensePrediction ? (
+
+ {content}
+
+ );
+ }
+
+ return content;
+};
diff --git a/src/shared/components/annotation/genomeNexus/MutationAssessor.tsx b/src/shared/components/annotation/genomeNexus/MutationAssessor.tsx
index 4665e3f3e37..76dfb84eb66 100644
--- a/src/shared/components/annotation/genomeNexus/MutationAssessor.tsx
+++ b/src/shared/components/annotation/genomeNexus/MutationAssessor.tsx
@@ -19,7 +19,8 @@ export default class MutationAssessor extends React.Component<
IMutationAssessorProps,
{}
> {
- static MUTATION_ASSESSOR_URL: string = 'http://mutationassessor.org/r3/';
+ // TODO Replace to new url when manuscript is available
+ // static MUTATION_ASSESSOR_URL: string = 'http://mutationassessor.org/r3/';
constructor(props: IMutationAssessorProps) {
super(props);
@@ -27,16 +28,6 @@ export default class MutationAssessor extends React.Component<
this.tooltipContent = this.tooltipContent.bind(this);
}
- public static download(
- mutationAssessorData: MutationAssessorData | undefined
- ): string {
- if (mutationAssessorData) {
- return `impact: ${mutationAssessorData.functionalImpact}, score: ${mutationAssessorData.functionalImpactScore}`;
- } else {
- return 'NA';
- }
- }
-
public render() {
let maContent: JSX.Element = (
@@ -44,7 +35,7 @@ export default class MutationAssessor extends React.Component<
if (
this.props.mutationAssessor &&
- this.props.mutationAssessor.functionalImpact !== null
+ this.props.mutationAssessor.functionalImpactPrediction !== null
) {
const maData = this.props.mutationAssessor;
maContent = (
@@ -52,7 +43,7 @@ export default class MutationAssessor extends React.Component<
className={classNames(
annotationStyles['annotation-item-text'],
(mutationAssessorColumn as any)[
- `ma-${maData.functionalImpact}`
+ `ma-${maData.functionalImpactPrediction}`
]
)}
>
@@ -80,15 +71,14 @@ export default class MutationAssessor extends React.Component<
private tooltipContent() {
if (this.props.mutationAssessor) {
const maData = this.props.mutationAssessor;
- const impact = maData.functionalImpact ? (
+ const impact = maData.functionalImpactPrediction ? (
+
+
+
+ ) : null;
+
+ return {impact};
+ };
+
+ let content: JSX.Element = (
+
+ );
+
+ if (alphaMissensePrediction && alphaMissensePrediction.length > 0) {
+ content = (
+
+
+
+ );
+ const arrowContent = ;
+ content = (
+ | Source | ++ AlphaMissense + | +
| Impact | ++ + {alphaMissensePrediction} + + | +
| Score | ++ {alphaMissenseScore.toFixed(2)} + | +
| Source | - - MutationAssessor - + {/* TODO Add link when manuscript is available */} + Mutation Assessor | |||
|
+
+ |
+ );
+ };
+
+ const renderImpactRow = (
+ iconClass: string,
+ impactData: string[],
+ showMutationAssessor: boolean,
+ key: number
+ ) => {
+ return (
+ ||||
|---|---|---|---|---|
| + + + + | + {showMutationAssessor && ( +{impactData[0]} | + )} +{impactData[1]} | +{impactData[2]} | +{impactData[3]} | +
| Legend | - {showMutationAssessor && ( -
-
- this.setState({
- active: 'mutationAssessor',
- })
- }
- >
- })
-
- |
+ {showMutationAssessor &&
+ renderHeaderIcon(
+ FunctionalImpactColumnName.MUTATION_ASSESSOR,
+ require('./mutationAssessor.png'),
+ () =>
+ setActive(
+ FunctionalImpactColumnName.MUTATION_ASSESSOR
+ )
+ )}
+ {renderHeaderIcon(
+ FunctionalImpactColumnName.SIFT,
+ require('./siftFunnel.png'),
+ () => setActive(FunctionalImpactColumnName.SIFT)
+ )}
+ {renderHeaderIcon(
+ FunctionalImpactColumnName.POLYPHEN2,
+ require('./polyPhen-2.png'),
+ () =>
+ setActive(
+ FunctionalImpactColumnName.POLYPHEN2
+ )
+ )}
+ {renderHeaderIcon(
+ FunctionalImpactColumnName.ALPHAMISSENSE,
+ require('./alphaMissenseGoogleDeepmind.png'),
+ () =>
+ setActive(
+ FunctionalImpactColumnName.ALPHAMISSENSE
+ )
)}
-
-
- this.setState({ active: 'sift' })
- }
- >
- })
-
- |
-
-
- this.setState({ active: 'polyPhen2' })
- }
- >
- })
-
- |
|---|---|---|---|
| - - - - | - {showMutationAssessor && ( -- high - | - )} -- deleterious - | -- probably_damaging - | -
| - - - - | -- medium - | -- | -- | -
| - - - - | - {showMutationAssessor && ( -- low - | - )} -- deleterious_low_confidence - | -- possibly_damaging - | -
| - - - - | - {showMutationAssessor && ( -- neutral - | - )} -- tolerated_low_confidence - | -- benign - | -
| - - - - | - {showMutationAssessor &&- | } -- tolerated - | -- | -
-
- Mutation Assessor
- {' '}
- predicts the functional impact of amino-acid substitutions in
- proteins, such as mutations discovered in cancer or missense
- polymorphisms. The functional impact is assessed based on
- evolutionary conservation of the affected amino acid in protein
- homologs. The method has been validated on a large set (60k) of
- disease associated (OMIM) and polymorphic variants.
-
- );
- }
-
- public static siftText() {
- return (
-
-
- SIFT
- {' '}
- predicts whether an amino acid substitution affects protein
- function based on sequence homology and the physical properties
- of amino acids. SIFT can be applied to naturally occurring
- nonsynonymous polymorphisms and laboratory-induced missense
- mutations.
-
- );
- }
-
- public static polyPhen2Text() {
- return (
-
-
- PolyPhen-2
- {' '}
- (Polymorphism Phenotyping v2) is a tool which predicts possible
- impact of an amino acid substitution on the structure and
- function of a human protein using straightforward physical and
- comparative considerations.
-
- );
- }
-
- public render() {
- return (
-
- {this.state.active === 'mutationAssessor' &&
- FunctionalImpactColumnTooltip.mutationAssessorText()}
- {this.state.active === 'sift' &&
- FunctionalImpactColumnTooltip.siftText()}
- {this.state.active === 'polyPhen2' &&
- FunctionalImpactColumnTooltip.polyPhen2Text()}
- {this.legend()}
-
- );
- }
-}
+ return (
+
+ {active === FunctionalImpactColumnName.MUTATION_ASSESSOR && (
+
+ );
+};
export function placeArrow(tooltipEl: any) {
const arrowEl = tooltipEl.querySelector('.rc-tooltip-arrow');
@@ -383,7 +288,11 @@ export default class FunctionalImpactColumnFormatter {
{showMutationAssessor && (
+ Mutation Assessor predicts the functional impact of
+ amino-acid substitutions in proteins, such as mutations
+ discovered in cancer or missense polymorphisms. The
+ functional impact is assessed based on evolutionary
+ conservation of the affected amino acid in protein homologs.
+ The method has been validated on a large set of disease
+ associated and polymorphic variants (
+
+ ClinVar
+
+ ).
+
+ + Mutation Assessor V4 data is available in the portal + since Oct. 8, 2024. + {' '} + New manuscript is in progress. Click{` `} + + here + + {` `} to see information about V3 data. +
+ )}
+ {active === FunctionalImpactColumnName.SIFT && (
+ + + Mutation Assessor V4 data is available in the portal + since Oct. 8, 2024. + {' '} + New manuscript is in progress. Click{` `} + + here + + {` `} to see information about V3 data. +
+
+ SIFT
+ {' '}
+ predicts whether an amino acid substitution affects protein
+ function based on sequence homology and the physical
+ properties of amino acids. SIFT can be applied to naturally
+ occurring nonsynonymous polymorphisms and laboratory-induced
+ missense mutations.
+
+ )}
+ {active === FunctionalImpactColumnName.POLYPHEN2 && (
+
+
+ PolyPhen-2
+ {' '}
+ (Polymorphism Phenotyping v2) is a tool which predicts
+ possible impact of an amino acid substitution on the
+ structure and function of a human protein using
+ straightforward physical and comparative considerations.
+
+ )}
+ {active === FunctionalImpactColumnName.ALPHAMISSENSE && (
+
+
+ AlphaMissense
+ {' '}
+ predicts the probability of a missense single nucleotide
+ variant being pathogenic and classifies it as either likely
+ benign, likely pathogenic, or uncertain.
+
+ )}
+ {legend()}
+ })
+
+
);
}
- public static getData(
+ static getData(
data: Mutation[],
- siftPolyphenCache: GenomeNexusCache,
- mutationAssessorCache: GenomeNexusMutationAssessorCache
+ cache?: GenomeNexusCache,
+ selectedTranscriptId?: string
): FunctionalImpactData {
- const siftPolyphenCacheData = FunctionalImpactColumnFormatter.getDataFromCache(
- data,
- siftPolyphenCache
- );
- const mutationAssessorCacheData = shouldShowMutationAssessor()
- ? FunctionalImpactColumnFormatter.getDataFromCache(
- data,
- mutationAssessorCache
- )
- : null;
-
- const siftData = siftPolyphenCacheData
- ? this.getSiftData(siftPolyphenCacheData.data)
- : undefined;
- const polyphenData = siftPolyphenCacheData
- ? this.getPolyphenData(siftPolyphenCacheData.data)
- : undefined;
- const mutationAssessor = mutationAssessorCacheData
- ? this.getMutationAssessorData(mutationAssessorCacheData.data)
- : undefined;
-
- const siftScore = siftData && siftData.siftScore;
- const siftPrediction = siftData && siftData.siftPrediction;
- const polyPhenScore = polyphenData && polyphenData.polyPhenScore;
- const polyPhenPrediction =
- polyphenData && polyphenData.polyPhenPrediction;
-
- const functionalImpactData: FunctionalImpactData = {
- mutationAssessor,
- siftScore,
- siftPrediction,
- polyPhenScore,
- polyPhenPrediction,
- };
- return functionalImpactData;
- }
-
- public static getSiftData(siftDataCache: VariantAnnotation | null) {
- let siftScore: number | undefined = undefined;
- let siftPrediction: string | undefined = undefined;
-
- if (
- siftDataCache &&
- !_.isEmpty(siftDataCache.transcript_consequences)
- ) {
- siftScore = siftDataCache.transcript_consequences[0].sift_score;
- siftPrediction =
- siftDataCache.transcript_consequences[0].sift_prediction;
+ const cacheData = this.getDataFromCache(data, cache);
+ if (!cacheData?.data) {
+ return {} as FunctionalImpactData;
}
- return {
- siftScore,
- siftPrediction,
- };
- }
-
- public static getPolyphenData(polyphenDataCache: VariantAnnotation | null) {
- let polyPhenScore: number | undefined = undefined;
- let polyPhenPrediction: string | undefined = undefined;
-
- if (
- polyphenDataCache &&
- !_.isEmpty(polyphenDataCache.transcript_consequences)
- ) {
- polyPhenScore =
- polyphenDataCache.transcript_consequences[0].polyphen_score;
- polyPhenPrediction =
- polyphenDataCache.transcript_consequences[0]
- .polyphen_prediction;
- }
+ const transcript = selectedTranscriptId
+ ? cacheData.data.transcript_consequences.find(
+ tc => tc.transcript_id === selectedTranscriptId
+ )
+ : undefined;
return {
- polyPhenScore,
- polyPhenPrediction,
+ mutationAssessor: shouldShowMutationAssessor()
+ ? cacheData.data.mutation_assessor
+ : undefined,
+ siftScore: transcript?.sift_score,
+ siftPrediction: transcript?.sift_prediction,
+ polyPhenScore: transcript?.polyphen_score,
+ polyPhenPrediction: transcript?.polyphen_prediction,
+ alphaMissenseScore: transcript?.alphaMissense?.score,
+ alphaMissensePrediction: transcript?.alphaMissense?.pathogenicity,
};
}
- public static getMutationAssessorData(
- mutationAssessorDataCache: VariantAnnotation | null
- ): MutationAssessorData | undefined {
- if (!mutationAssessorDataCache) {
- return undefined;
- } else {
- return mutationAssessorDataCache.mutation_assessor
- ? mutationAssessorDataCache.mutation_assessor.annotation
- : undefined;
- }
- }
-
public static renderFunction(
data: Mutation[],
- siftPolyphenCache: GenomeNexusCache | undefined,
- mutationAssessorCache: GenomeNexusMutationAssessorCache | undefined
+ genomeNexusCache: GenomeNexusCache | undefined,
+ selectedTranscriptId?: string
) {
const showMutationAssessor = shouldShowMutationAssessor();
- const siftPolyphenCacheData = FunctionalImpactColumnFormatter.getDataFromCache(
- data,
- siftPolyphenCache
- );
- const mutationAssessorCacheData = showMutationAssessor
- ? FunctionalImpactColumnFormatter.getDataFromCache(
- data,
- mutationAssessorCache
- )
- : null;
return (
{showMutationAssessor &&
FunctionalImpactColumnFormatter.makeFunctionalImpactViz(
- mutationAssessorCacheData,
- FunctionalImpactColumnsName.MUTATION_ASSESSOR
+ data,
+ FunctionalImpactColumnName.MUTATION_ASSESSOR,
+ genomeNexusCache,
+ selectedTranscriptId
)}
{FunctionalImpactColumnFormatter.makeFunctionalImpactViz(
- siftPolyphenCacheData,
- FunctionalImpactColumnsName.SIFT
+ data,
+ FunctionalImpactColumnName.SIFT,
+ genomeNexusCache,
+ selectedTranscriptId
)}
{FunctionalImpactColumnFormatter.makeFunctionalImpactViz(
- siftPolyphenCacheData,
- FunctionalImpactColumnsName.POLYPHEN2
+ data,
+ FunctionalImpactColumnName.POLYPHEN2,
+ genomeNexusCache,
+ selectedTranscriptId
+ )}
+ {FunctionalImpactColumnFormatter.makeFunctionalImpactViz(
+ data,
+ FunctionalImpactColumnName.ALPHAMISSENSE,
+ genomeNexusCache,
+ selectedTranscriptId
)}
);
}
- public static download(
+ static download(
data: Mutation[],
- siftPolyphenCache: GenomeNexusCache,
- mutationAssessorCache: GenomeNexusMutationAssessorCache
+ cache: GenomeNexusCache,
+ selectedTranscriptId?: string
): string {
- if (siftPolyphenCache || mutationAssessorCache) {
- const functionalImpactData = FunctionalImpactColumnFormatter.getData(
- data,
- siftPolyphenCache,
- mutationAssessorCache
- );
- let downloadData = [];
- if (functionalImpactData) {
- if (shouldShowMutationAssessor()) {
- downloadData.push(
- `MutationAssessor: ${MutationAssessor.download(
- functionalImpactData.mutationAssessor
- )}`
- );
- }
- downloadData = downloadData.concat([
- `SIFT: ${Sift.download(
- functionalImpactData.siftScore,
- functionalImpactData.siftPrediction
- )}`,
- `Polyphen-2: ${PolyPhen2.download(
- functionalImpactData.polyPhenScore,
- functionalImpactData.polyPhenPrediction
- )}`,
- ]);
- return downloadData.join(';');
- }
- }
- return '';
+ const functionalImpactData = this.getData(
+ data,
+ cache,
+ selectedTranscriptId
+ );
+ if (!functionalImpactData) return '';
+
+ const downloadData = [
+ shouldShowMutationAssessor() &&
+ `MutationAssessor: ${
+ functionalImpactData.mutationAssessor
+ ? `impact: ${functionalImpactData.mutationAssessor.functionalImpactPrediction}, score: ${functionalImpactData.mutationAssessor.functionalImpactScore}`
+ : 'NA'
+ }`,
+ `SIFT: ${
+ functionalImpactData.siftScore ||
+ functionalImpactData.siftPrediction
+ ? `impact: ${functionalImpactData.siftPrediction}, score: ${functionalImpactData.siftScore}`
+ : 'NA'
+ }`,
+ `Polyphen-2: ${
+ functionalImpactData.polyPhenScore ||
+ functionalImpactData.polyPhenPrediction
+ ? `impact: ${functionalImpactData.polyPhenPrediction}, score: ${functionalImpactData.polyPhenScore}`
+ : 'NA'
+ }`,
+ `AlphaMissense: ${
+ functionalImpactData.alphaMissenseScore ||
+ functionalImpactData.alphaMissensePrediction
+ ? `pathogenicity: ${functionalImpactData.alphaMissensePrediction}, score: ${functionalImpactData.alphaMissenseScore}`
+ : 'NA'
+ }`,
+ ];
+
+ return downloadData.join(';');
}
private static getDataFromCache(
data: Mutation[],
- cache: GenomeNexusCache | GenomeNexusMutationAssessorCache | undefined
+ cache: GenomeNexusCache | GenomeNexusCache | undefined
): GenomeNexusCacheDataType | null {
if (data.length === 0 || !cache) {
return null;
@@ -623,11 +502,13 @@ export default class FunctionalImpactColumnFormatter {
}
private static makeFunctionalImpactViz(
- cacheData: GenomeNexusCacheDataType | null,
- column: FunctionalImpactColumnsName
+ mutation: Mutation[],
+ column: FunctionalImpactColumnName,
+ genomeNexusCache?: GenomeNexusCache,
+ selectedTranscriptId?: string
) {
let status: TableCellStatus | null = null;
-
+ const cacheData = this.getDataFromCache(mutation, genomeNexusCache);
if (cacheData === null) {
status = TableCellStatus.LOADING;
} else if (cacheData.status === 'error') {
@@ -635,36 +516,38 @@ export default class FunctionalImpactColumnFormatter {
} else if (cacheData.data === null) {
status = TableCellStatus.NA;
} else {
- let functionalImpactData;
+ const data = this.getData(
+ mutation,
+ genomeNexusCache,
+ selectedTranscriptId
+ );
switch (column) {
- case FunctionalImpactColumnsName.MUTATION_ASSESSOR:
- functionalImpactData = FunctionalImpactColumnFormatter.getMutationAssessorData(
- cacheData.data
- );
+ case FunctionalImpactColumnName.MUTATION_ASSESSOR:
return (
+ Horizontal Axis:
+ {`${horzAxisDataSampleCount} samples from ${
+ horzAxisStudies.length
+ } ${Pluralize('study', horzAxisStudies.length)}`}
+
+ );
+ }
+ break;
default:
// molecular profile
if (
@@ -731,6 +758,31 @@ export default class PlotsTab extends React.Component
+ Vertical Axis:
+ {`${vertAxisDataSampleCount} samples from ${
+ vertAxisStudies.length
+ } ${Pluralize('study', vertAxisStudies.length)}`}
+
+ );
+ }
+ break;
case CLIN_ATTR_DATA_TYPE:
if (
this.vertSelection.dataSourceId !== undefined &&
@@ -1121,9 +1173,10 @@ export default class PlotsTab extends React.Component
-
+
+ {this.currentResourceDatum.sampleId + ? this.currentResourceDatum.sampleId + : this.currentResourceDatum.patientId} + {this.currentResourceDatum.resourceDefinition + .description && + ` | ${this.currentResourceDatum.resourceDefinition.description}`} +
+ boolean;
openResource: (resource: ResourceData) => void;
+ sampleId?: React.ReactNode;
}
function icon(resource: ResourceData) {
@@ -45,7 +46,7 @@ function icon(resource: ResourceData) {
}
const ResourceTable = observer(
- ({ resources, isTabOpen, openResource }: IResourceTableProps) => {
+ ({ resources, isTabOpen, openResource, sampleId }: IResourceTableProps) => {
const resourceTable = useLocalObservable(() => ({
get data() {
return _.sortBy(resources, r => r.resourceDefinition.priority);
@@ -56,6 +57,7 @@ const ResourceTable = observer(