OncoKB Updates

package.json

@@ -219,7 +219,7 @@
     "mobxpromise": "github:cbioportal/mobxpromise#303db72588860bff0a6862a4f07a4e8a3578c94f",
     "numeral": "^2.0.6",
     "object-sizeof": "^1.2.0",
-    "oncokb-styles": "~1.3.0",
+    "oncokb-styles": "~1.4.2",
     "oncokb-ts-api-client": "^1.3.1",
     "oncoprintjs": "^6.0.0",
     "pako": "2.0.2",

packages/react-mutation-mapper/package.json

@@ -47,7 +47,7 @@
     "lodash": "^4.17.15",
     "memoize-weak-decorator": "^1.0.3",
     "mobxpromise": "github:cbioportal/mobxpromise#303db72588860bff0a6862a4f07a4e8a3578c94f",
-    "oncokb-styles": "~1.3.0",
+    "oncokb-styles": "~1.4.2",
     "oncokb-ts-api-client": "^1.3.1",
     "react-collapse": "^4.0.3",
     "react-if": "^2.1.0",

packages/react-mutation-mapper/src/component/oncokb/CompactAnnotationIcon.tsx

@@ -7,7 +7,6 @@ import { normalizeLevel, normalizeOncogenicity } from '../../util/OncoKbUtils';
 const BIOLOGICAL_COLOR_MAP: { [level: string]: string } = {
     oncogenic: '#0968C3',
     'likely-oncogenic': '#0968C3',
-    'predicted-oncogenic': '#0968C3',
     resistance: '#0968C3',
     neutral: '#696969',
     'likely-neutral': '#696969',

packages/react-mutation-mapper/src/component/oncokb/OncoKBSuggestAnnotationLinkout.tsx

@@ -13,7 +13,7 @@ export default class OncoKBSuggestAnnotationLinkout extends React.Component<{
                 <span> but hasn't been curated yet. Please feel free to </span>
                 <a
                     target="_blank"
-                    href={`mailto:contact@oncokb.org?subject=Annotation suggestion for ${this.props.gene}&&body=Thank you for using OncoKB.%0APlease provide the following information for ${this.props.gene} curation:%0A%0AEvidence:%0APMIDs:%0AAbstracts:`}
+                    href={`mailto:contact@oncokb.org?subject=Annotation suggestion for ${this.props.gene}&&body=Thank you for using OncoKB™.%0APlease provide the following information for ${this.props.gene} curation:%0A%0AEvidence:%0APMIDs:%0AAbstracts:`}
                     title="suggest to annotate this gene"
                 >
                     suggest the team annotate the gene

packages/react-mutation-mapper/src/component/oncokb/OncoKbCard.tsx

@@ -5,7 +5,7 @@ import * as React from 'react';
 
 import { ICache } from '../../model/SimpleCache';
 
-import oncoKbLogoImgSrc from '../../images/oncokb.svg';
+import oncoKbLogoImgSrc from 'oncokb-styles/dist/images/logo/oncokb.svg';
 import mainStyles from './main.module.scss';
 import { OncoKbCardTitle } from './OncoKbCardTitle';
 import { OncoKbCardBody } from './OncoKbCardBody';
@@ -50,7 +50,7 @@ export default class OncoKbCard extends React.Component<OncoKbCardProps> {
             <img
                 src={oncoKbLogoImgSrc}
                 className={mainStyles['oncokb-logo']}
-                alt="OncoKB"
+                alt="OncoKB™"
             />
         );
         return (

packages/react-mutation-mapper/src/component/oncokb/OncoKbCardBody.tsx

@@ -33,7 +33,7 @@ const ONCOKB_DATA_ACCESS_PAGE_LINK =
 const publicInstanceDisclaimerOverLay = (
     <div>
         <p>
-            This cBioPortal instance is not linked to an OncoKB license, and
+            This cBioPortal instance is not linked to an OncoKB™ license, and
             therefore some OncoKB content is not available including
             therapeutic, diagnostic and prognostic implications. To obtain a
             license, please follow{' '}

packages/react-mutation-mapper/src/component/oncokb/OncoKbFeedback.tsx

@@ -31,7 +31,7 @@ export default class OncoKbFeedback extends React.Component<
                 onHide={this.props.handleFeedbackClose}
             >
                 <Modal.Header closeButton>
-                    <Modal.Title>OncoKB Annotation Feedback</Modal.Title>
+                    <Modal.Title>OncoKB™ Annotation Feedback</Modal.Title>
                 </Modal.Header>
                 <Modal.Body>
                     <iframe

packages/react-mutation-mapper/src/component/track/OncoKbTrack.tsx

@@ -11,7 +11,7 @@ import { default as Track, TrackProps } from './Track';
 import { TrackItemSpec } from './TrackItem';
 import { Mutation } from 'cbioportal-utils';
 
-import oncoKbImg from '../../images/oncogenic-only.svg';
+import oncoKbImg from 'oncokb-styles/dist/images/oncogenic.svg';
 
 type OncoKbTrackProps = TrackProps & {
     store: MutationMapperStore<Mutation>;
@@ -68,7 +68,7 @@ export default class OncoKbTrack extends React.Component<OncoKbTrackProps, {}> {
         return (
             <span>
                 <span style={{ marginRight: 2 }}>{getOncoKbImage()}</span>
-                OncoKB
+                OncoKB™
             </span>
         );
     }

packages/react-mutation-mapper/src/component/track/TrackSelector.tsx

@@ -76,7 +76,7 @@ export default class TrackSelector extends React.Component<
             [TrackName.OncoKB]: {
                 label: (
                     <span>
-                        OncoKB
+                        OncoKB™
                         {this.isPending(TrackName.OncoKB) && this.loaderIcon()}
                     </span>
                 ),

packages/react-mutation-mapper/src/util/OncoKbUtils.ts

@@ -14,7 +14,6 @@ const ONCOGENIC_CLASS_NAMES: { [oncogenic: string]: string } = {
     Unknown: 'unknown',
     Inconclusive: 'inconclusive',
     Resistance: 'oncogenic',
-    'Predicted Oncogenic': 'oncogenic',
     'Likely Oncogenic': 'oncogenic',
     Oncogenic: 'oncogenic',
 };
@@ -26,7 +25,6 @@ const ONCOGENIC_SCORE: { [oncogenic: string]: number } = {
     Inconclusive: 0,
     'Likely Neutral': 0,
     Resistance: 5,
-    'Predicted Oncogenic': 5,
     'Likely Oncogenic': 5,
     Oncogenic: 5,
 };
@@ -107,7 +105,6 @@ export function oncogenicYPosition(
 ) {
     const oncogenicityMap: { [id: string]: number } = {
         Oncogenic: 0,
-        'Predicted Oncogenic': 0,
         'Likely Oncogenic': 0,
         Resistance: 0,
         Neutral: 1,

packages/react-variant-view/package.json

@@ -47,7 +47,7 @@
     "jquery": "^3.2.1",
     "lodash": "^4.17.15",
     "mobxpromise": "github:cbioportal/mobxpromise#303db72588860bff0a6862a4f07a4e8a3578c94f",
-    "oncokb-styles": "~0.1.2",
+    "oncokb-styles": "~1.4.2",
     "oncokb-ts-api-client": "^1.3.1",
     "react-bootstrap": "^0.31.5",
     "react-collapse": "4.0.3",

packages/react-variant-view/src/component/headerAnnotation/HeaderAnnotation.tsx

@@ -19,7 +19,7 @@ import { ANNOTATION_QUERY_FIELDS } from '../../util/Constants';
 import headerAnnotationStyle from './HeaderAnnotation.module.scss';
 import { generateOncokbLink, ONCOKB_URL } from '../pathogenicity/Oncokb';
 import TranscriptSummaryTable from './TranscriptSummaryTable';
-import oncokbLogo from '../../image/oncokb.png';
+import oncokbLogo from 'oncokb-styles/dist/images/oncogenic.svg';
 
 interface IHeaderAnnotationProps {
     annotation: VariantAnnotationSummary | undefined;
@@ -410,7 +410,7 @@ export default class HeaderAnnotation extends React.Component<
                                         alignItems: 'center',
                                     }}
                                 >
-                                    OncoKB
+                                    OncoKB™
                                     <img
                                         height={12}
                                         src={oncokbLogo}

packages/react-variant-view/src/component/pathogenicity/Oncokb.tsx

@@ -13,7 +13,7 @@ interface IOncokbProps {
 export enum ONCOGENICITY {
     ONCOGENIC = 'Oncogenic',
     LIKELY_ONCOGENIC = 'Likely Oncogenic',
-    PREDICTED_ONCOGENIC = 'Predicted Oncogenic',
+    RESISTANCE = 'Resistance',
     NEUTRAL = 'Neutral',
     LIKELY_NEUTRAL = 'Likely Neutral',
     INCONCLUSIVE = 'Inconclusive',
@@ -24,7 +24,7 @@ export enum ONCOGENICITY {
 export const ONCOGENICITY_CLASS_NAMES: { [oncogenic: string]: string } = {
     [ONCOGENICITY.ONCOGENIC]: 'oncogenic',
     [ONCOGENICITY.LIKELY_ONCOGENIC]: 'oncogenic',
-    [ONCOGENICITY.PREDICTED_ONCOGENIC]: 'oncogenic',
+    [ONCOGENICITY.RESISTANCE]: 'oncogenic',
     [ONCOGENICITY.NEUTRAL]: 'neutral',
     [ONCOGENICITY.LIKELY_NEUTRAL]: 'neutral',
     [ONCOGENICITY.INCONCLUSIVE]: 'inconclusive',
@@ -82,7 +82,7 @@ export default class Oncokb extends React.Component<IOncokbProps> {
                             target="_blank"
                             rel="noopener noreferrer"
                         >
-                            OncoKB
+                            OncoKB™
                         </a>{' '}
                         is a precision oncology knowledge base that contains
                         <br />

packages/react-variant-view/src/component/therapeuticImplication/TherapeuticImplication.tsx

@@ -101,7 +101,7 @@ class TherapeuticImplication extends React.Component<
                             target="_blank"
                             rel="noopener noreferrer"
                         >
-                            OncoKB
+                            OncoKB™
                         </a>
                         &nbsp;is a precision oncology knowledge base that
                         contains

src/pages/resultsView/ResultsViewPageStoreUtils.ts

@@ -322,7 +322,6 @@ export function compileStructuralVariants<
 
 export const ONCOKB_ONCOGENIC_LOWERCASE = [
     'likely oncogenic',
-    'predicted oncogenic',
     'oncogenic',
     'resistance',
 ];

src/pages/staticPages/tools/mutationMapper/MutationMapperTool.tsx

@@ -705,7 +705,7 @@ export default class MutationMapperTool extends React.Component<
                 Genome build GRCh38 is currently in beta. Several annotation
                 sources displayed on the page might not have official GRCh38
                 support i.e.&nbsp;
-                <a href={ONCOKB_URL}>OncoKB</a>,&nbsp;
+                <a href={ONCOKB_URL}>OncoKB™</a>,&nbsp;
                 <a href={CIVIC_URL}>CIViC</a>,&nbsp;
                 <a href={CANCER_HOTSPOTS_URL}>Cancer Hotspots</a>,&nbsp;
                 <a href={MY_CANCER_GENOME_URL}>My Cancer Genome</a> and&nbsp;

src/pages/studyView/oncokb/OncoKBUtils.tsx

@@ -1,8 +1,6 @@
 import * as React from 'react';
 import { If, Then, Else } from 'react-if';
 
-const oncoKbImg = require('shared/components/annotation/images/oncogenic-only.svg');
-
 const ONCOKB_URL = 'https://oncokb.org';
 
 export function getOncoKBReferenceInfo(
@@ -56,11 +54,7 @@ export function getOncoKBReferenceInfo(
 export function getOncoKBCancerGeneListLinkout() {
     return (
         <a href={`${ONCOKB_URL}/cancerGenes`} target="_blank">
-            OncoKB Cancer Gene List
+            OncoKB™ Cancer Gene List
         </a>
     );
 }
-
-export function getOncoKbImage() {
-    return <img src={oncoKbImg} alt="OncoKB Oncogenic Symbol" />;
-}

src/shared/components/driverAnnotations/DriverAnnotationControls.tsx

@@ -129,13 +129,13 @@ export default class DriverAnnotationControls extends React.Component<
                                         <DefaultTooltip
                                             overlay={
                                                 <span>
-                                                    Oncogenicity from OncoKB
+                                                    Oncogenicity from OncoKB™
                                                 </span>
                                             }
                                             placement="top"
                                         >
                                             <img
-                                                src={require('../../../rootImages/oncokb.png')}
+                                                src={require('oncokb-styles/dist/images/logo/oncokb.svg')}
                                                 style={{
                                                     maxHeight: '12px',
                                                     cursor: 'pointer',

src/shared/components/mutationTable/column/annotation/AnnotationHeader.tsx

@@ -29,7 +29,7 @@ enum OncokbOncogenicIconEnum {
 
 const oncokbOncogenicDescription: _.Dictionary<string> = {
     [OncokbOncogenicIconEnum.ONCOGENIC]:
-        'Oncogenic/Likely Oncogenic/Predicted Oncogenic/Resistance',
+        'Oncogenic/Likely Oncogenic/Resistance',
     [OncokbOncogenicIconEnum.NUETRAL]: 'Likely Neutral',
     [OncokbOncogenicIconEnum.INCONCLUSIVE]: 'Inconclusive',
     [OncokbOncogenicIconEnum.VUS]: 'VUS',
@@ -61,7 +61,7 @@ export const sourceTooltipInfo = {
     [AnnotationSources.ONCOKB]: [
         {
             sourceUrl: 'https://www.oncokb.org/',
-            sourceName: 'OncoKB',
+            sourceName: 'OncoKB™',
             sourceDescription:
                 'a precision oncology knowledge base that contains information about the effects and treatment implications of variants in cancer',
             reference: 'Chakravarty et al. 2017',

src/shared/components/oncoprint/ResultsViewOncoprintUtils.tsx

@@ -42,9 +42,9 @@ export function getAnnotatingProgressMessage(
 ) {
     let message;
     if (usingOncokb && usingHotspot) {
-        message = 'Annotating with OncoKB and Cancer Hotspots';
+        message = 'Annotating with OncoKB™ and Cancer Hotspots';
     } else if (usingOncokb) {
-        message = 'Annotating with OncoKB';
+        message = 'Annotating with OncoKB™';
     } else if (usingHotspot) {
         message = 'Annotating with Cancer Hotspots';
     } else {

src/shared/lib/StoreUtils.spec.ts

@@ -1420,14 +1420,6 @@ describe('StoreUtils', () => {
                 'Oncogenic'
             );
         });
-        it('should return Predicted Oncogenic if thats the input', () => {
-            assert.equal(
-                getOncoKbOncogenic({
-                    oncogenic: 'Predicted Oncogenic',
-                } as IndicatorQueryResp),
-                'Predicted Oncogenic'
-            );
-        });
         it('should return Resistance if thats the input', () => {
             assert.equal(
                 getOncoKbOncogenic({

yarn.lock

@@ -17390,15 +17390,10 @@ once@~1.3.0:
   dependencies:
     wrappy "1"
 
-oncokb-styles@~0.1.2:
-  version "0.1.2"
-  resolved "https://registry.yarnpkg.com/oncokb-styles/-/oncokb-styles-0.1.2.tgz#8b26c0a0829787cdc1b595d3a021b3266607102b"
-  integrity sha512-tuy5s3qFxgf1ogMATQSRPNgLlAMrvOOTCAN1dm/wJ+VZoStbJ7g36/qHwc99UPfh3vrB05broLodF+k58p5tUw==
-
-oncokb-styles@~1.3.0:
-  version "1.3.0"
-  resolved "https://registry.yarnpkg.com/oncokb-styles/-/oncokb-styles-1.3.0.tgz#3cf98a5d4e936b6ab384deb6be6753bec0c2e940"
-  integrity sha512-x+Foc05kr9kjeaFwUz4JkG7D5maUgEG9b2GBjH5JdFfRCw+yn40H8APLZ3D4XgxX4OG5EUTnvxZP/gr72brdfw==
+oncokb-styles@~1.4.2:
+  version "1.4.2"
+  resolved "https://registry.yarnpkg.com/oncokb-styles/-/oncokb-styles-1.4.2.tgz#ad601699636875abe425d80b25c050d28d47c2bc"
+  integrity sha512-dq/w/OZv7oTjQzyXRo54ldC3PiHHu36eVuFmS0U5PGlk3Qx8XfB9XSwELHKTgmuen5H8YKQJxc/h3cBlFBF7Xw==
 
 oncoprintjs@^5.0.2:
   version "5.0.3"