Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update packages #159

Merged
merged 1 commit into from
Jul 8, 2024
Merged

Update packages #159

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 8 additions & 4 deletions package.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,12 +21,12 @@
"@types/superagent": "^4.1.1",
"autobind-decorator": "^2.4.0",
"bootstrap": "^4.3.1",
"cbioportal-frontend-commons": "^0.5.51",
"cbioportal-utils": "^0.3.34",
"cbioportal-frontend-commons": "^0.5.67",
"cbioportal-utils": "^0.3.41",
"classnames": "^2.2.6",
"file-loader": "^4.3.0",
"font-awesome": "^4.7.0",
"genome-nexus-ts-api-client": "^1.1.28",
"genome-nexus-ts-api-client": "1.1.32",
"lodash": "^4.17.21",
"mobx": "^6.0.0",
"mobx-react": "^6.0.0",
Expand All @@ -42,7 +42,7 @@
"react-bootstrap": "^1.0.0-beta.6",
"react-dom": "^16.14.0",
"react-markdown": "^7.0.1",
"react-mutation-mapper": "^0.8.93",
"react-mutation-mapper": "^0.8.110",
"react-router-bootstrap": "^0.24.4",
"react-router-dom": "^4.3.1",
"react-scripts": "^3.4.4",
Expand Down Expand Up @@ -85,5 +85,9 @@
},
"devDependencies": {
"@types/react-scroll": "^1.5.4"
},
"resolutions": {
"cheerio": "1.0.0-rc.10",
"parse5-htmlparser2-tree-adapter": "^6.0.0"
}
}
2 changes: 1 addition & 1 deletion src/component/variantPage/BasicInfo.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -437,7 +437,7 @@ export default class BasicInfo extends React.Component<IBasicInfoProps> {
>
{
annotationSummary.vues
.revisedVariantClassification
.revisedVariantClassificationStandard
}
</span>
</a>
Expand Down
32 changes: 16 additions & 16 deletions src/component/variantPage/ClinicalImplication.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,30 +1,30 @@
import _ from 'lodash';
// import _ from 'lodash';
import * as React from 'react';
import { observer } from 'mobx-react';

import { IndicatorQueryResp } from 'oncokb-ts-api-client';
import { ICivicVariantIndex, ICivicVariantSummary } from 'cbioportal-utils';
// import { ICivicVariantIndex, ICivicVariantSummary } from 'cbioportal-utils';

import OncoKb from './clinicalImplication/OncoKb';
import Civic from './clinicalImplication/Civic';
import Separator from '../Separator';
// import Civic from './clinicalImplication/Civic';
// import Separator from '../Separator';

interface IClinicalImplicationProps {
oncokb: IndicatorQueryResp | undefined;
civic?: ICivicVariantIndex;
// civic?: ICivicVariantIndex;
isCanonicalTranscriptSelected: boolean;
}

@observer
class ClinicalImplication extends React.Component<IClinicalImplicationProps> {
get civicVariant(): ICivicVariantSummary | undefined {
if (this.props.civic) {
// assuming the index only contains one variant
return _.values(_.values(this.props.civic)[0])[0];
} else {
return undefined;
}
}
// get civicVariant(): ICivicVariantSummary | undefined {
// if (this.props.civic) {
// // assuming the index only contains one variant
// return _.values(_.values(this.props.civic)[0])[0];
// } else {
// return undefined;
// }
// }

public render() {
return (
Expand All @@ -35,13 +35,13 @@ class ClinicalImplication extends React.Component<IClinicalImplicationProps> {
this.props.isCanonicalTranscriptSelected
}
/>
<Separator />
<Civic
{/* <Separator /> */}
{/* <Civic
civic={this.civicVariant}
isCanonicalTranscriptSelected={
this.props.isCanonicalTranscriptSelected
}
/>
/> */}
</>
);
}
Expand Down
2 changes: 1 addition & 1 deletion src/component/variantPage/FunctionalGroups.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ class FunctionalGroups extends React.Component<IFunctionalGroupsProps> {
<td>
<ClinicalImplication
oncokb={this.props.oncokb}
civic={this.props.civic}
// civic={this.props.civic}
isCanonicalTranscriptSelected={
this.props.isCanonicalTranscriptSelected
}
Expand Down
65 changes: 33 additions & 32 deletions src/component/variantPage/biologicalFunction/ReVUE.tsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,41 +12,42 @@ export const ReVUEContent: React.FunctionComponent<IReVUEProps> = (props) => {
return props.vue ? (
<div>
<div>
Predicted Effect by{` `}
{
<a
href="https://useast.ensembl.org/info/docs/tools/vep/index.html"
target="_blank"
rel="noopener noreferrer"
>
VEP
</a>
}
Predicted Effect by{' '}
<a
href="https://useast.ensembl.org/info/docs/tools/vep/index.html"
target="_blank"
rel="noopener noreferrer"
>
VEP
</a>
: <strong>{props.vue.defaultEffect}</strong>
</div>
<div>
Revised Protein Effect by{` `}
{
<a
href="https://cancerrevue.org"
target="_blank"
rel="noopener noreferrer"
>
reVUE
</a>
}
{` (`}
{
<a
href={`https://pubmed.ncbi.nlm.nih.gov/${props.vue.pubmedId}/`}
rel="noopener noreferrer"
target="_blank"
>
{props.vue.referenceText}
</a>
}
{`): `}
<strong>{props.vue.revisedProteinEffect}</strong>
Revised Protein Effect by{' '}
<a
href="https://cancerrevue.org"
target="_blank"
rel="noopener noreferrer"
>
reVUE
</a>{' '}
(
{props.vue.references.map((reference, index) => (
<React.Fragment key={reference.pubmedId}>
{index > 0 && ', '}
<a
href={`https://pubmed.ncbi.nlm.nih.gov/${reference.pubmedId}/`}
rel="noopener noreferrer"
target="_blank"
>
{reference.referenceText}
</a>
</React.Fragment>
))}
):{' '}
<strong>
{props.vue.revisedVariantClassificationStandard}
</strong>
</div>
</div>
) : (
Expand Down
Loading