react-mutation-mapper 0.8.60 → 0.8.62

package/dist/styles.css

@@ -1,48 +1,6 @@
 .gnomad-frequency-table .rt-table .rt-tbody .rt-td {
   padding: 4px 5px;
 }
-.oncokb-treatment-table {
-  font-size: 0.8rem;
-}
-.oncokb-treatment-table .rt-tbody {
-  line-height: 0.8rem;
-}
-.oncokb-tooltip {
-  background: none;
-}
-.oncokb-tooltip .rc-tooltip-inner {
-  padding: 0;
-  border-color: #DDDDDD;
-}
-
-.oncokb-card-tabs > .nav {
-  margin: 0 auto;
-  position: relative;
-  z-index: 1;
-  display: flex;
-}
-.oncokb-card-tabs > .nav > li > a {
-  padding: 7px 10px;
-}
-.oncokb-card-tabs > .nav > li a:focus {
-  outline-width: 0;
-}
-.oncokb-card-tabs > .nav > li:not(.active) a:hover {
-  background: none !important;
-  border-color: transparent !important;
-}
-.oncokb-card-tabs > .nav .active a {
-  border-top: 3px solid #0968C3 !important;
-  padding-top: 5px;
-}
-.oncokb-card-tabs > .tab-content {
-  padding: 10px 0;
-  min-height: 50px;
-  position: relative;
-}
-.oncokb-card-tabs .rt-thead .rt-resizable-header-content {
-  text-align: left;
-}
 .default-mutation-table {
   font-size: 0.8rem;
   min-width: 300px;
@@ -185,193 +143,6 @@
   list-style-position: inside;
   padding-left: 0;
 }
-.main-module_oncokb-card__32DzD {
-  margin: auto;
-  width: 600px;
-  font-size: 14px;
-  line-height: 18px;
-}
-
-.main-module_tab-content__8nUyf {
-  max-height: 300px;
-  overflow-y: auto;
-}
-
-.main-module_tooltip-refs__SpA4W {
-  max-width: 400px;
-  max-height: 400px;
-  overflow-y: auto;
-}
-
-.main-module_disclaimer__3CLlM {
-  color: grey;
-  font-style: italic;
-}
-
-.main-module_blue-icon__2Hs-v {
-  color: #0968C3;
-}
-
-.main-module_footer__2dc-8 {
-  display: flex;
-  justify-content: space-between;
-  padding: 5px 10px;
-}
-
-.main-module_oncokb-logo__3RVg7 {
-  height: 16px;
-}
-
-.main-module_title__2kT-n {
-  line-height: 22px;
-  font-size: 22px;
-  background-color: #0968C3;
-  color: #fff;
-  text-align: center;
-  padding: 5px 10px;
-}
-
-.main-module_additional-info__1nXTm {
-  padding: 5px 10px;
-  line-height: 20px;
-  border-bottom: 1px solid lightgrey;
-}
-
-.main-module_biological-info__2efDC {
-  display: flex;
-  flex-direction: row;
-  background-color: #064785;
-  color: white;
-  padding: 10px 0;
-  font-weight: bold;
-  text-align: center;
-}
-
-.main-module_ellipsis-text-wrapper__18dny {
-  overflow: hidden;
-  white-space: nowrap;
-  display: flex;
-  align-items: center;
-}
-.level-module_levels__2ZL1B {
-  padding: 5px 10px;
-  font-size: 12px;
-}
-
-.level-module_levels-li__1tgCC {
-  line-height: 16px;
-  margin: 3px 0;
-  display: flex;
-  align-items: flex-start;
-}
-.collapsible-module_collapsible-header__3nZtU {
-  cursor: pointer;
-  min-height: 30px;
-  line-height: 30px;
-  padding: 0 10px;
-  background-color: white;
-  border-bottom: 1px solid #DDDDDD;
-  border-top: 1px solid #DDDDDD;
-}
-
-.collapsible-module_levels-collapse__2GBRW {
-  border-bottom: 1px solid #DDDDDD;
-}
-.listGroupItem-module_list-group-item__1Y5zb {
-  border: 0;
-  padding: 5px 0;
-  font-size: 13px;
-  display: flex;
-  flex-direction: column;
-}
-.listGroupItem-module_list-group-item__1Y5zb a {
-  color: #0968C3;
-}
-
-.listGroupItem-module_list-group-item__1Y5zb:not(:first-child) {
-  border-top: 1px solid #DDDDDD;
-}
-
-.listGroupItem-module_list-group-item__1Y5zb:last-child {
-  border-bottom-right-radius: 0;
-  border-bottom-left-radius: 0;
-}
-
-.listGroupItem-module_list-group-item__1Y5zb:first-child {
-  border-top-left-radius: 0;
-  border-top-right-radius: 0;
-}
-
-.listGroupItem-module_list-group-item-title__3diZg {
-  line-height: 16px;
-}
-
-.listGroupItem-module_list-group-item-content__Sspft {
-  display: flex;
-  flex-direction: row;
-  justify-content: space-between;
-}
-
-.listGroupItem-module_no-style-ul__2Rf8i {
-  padding: 0;
-  margin-bottom: 0 !important;
-}
-.listGroupItem-module_no-style-ul__2Rf8i li {
-  list-style-type: none;
-}
-.tabs-module_tabs-wrapper__XKjzo {
-  display: flex;
-  flex-direction: column;
-}
-
-.tabs-module_tabs__2I3mz {
-  display: flex;
-  flex-direction: row;
-  background-color: #0b2569;
-  margin-bottom: 5px !important;
-  white-space: nowrap;
-  height: 45px;
-  padding: 0;
-}
-
-.tabs-module_tab__3MoDA {
-  flex-grow: 1;
-  text-align: center;
-  height: 45px;
-}
-
-.tabs-module_tab-pane__sGd85 {
-  padding: 0 10px 0 10px;
-}
-
-.tabs-module_tab-title-a__2WTNA {
-  color: white;
-  display: flex;
-  flex-direction: column;
-}
-
-.tabs-module_tab__3MoDA > a:hover {
-  text-decoration: none !important;
-}
-
-.tabs-module_tab-title-a__2WTNA:hover {
-  transition: color 0.28s ease;
-  color: white;
-}
-
-.tabs-module_tab-title__2z9-D {
-  line-height: 22px;
-  float: left;
-  color: white;
-  text-transform: uppercase;
-}
-
-.tabs-module_tab-subtitle__1P8B_ {
-  width: 100%;
-  line-height: 20px;
-  color: orange;
-  text-overflow: ellipsis;
-}
 .hotspotInfo-module_hotspot-info__S24fX {
   max-width: 400px;
   display: block;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "react-mutation-mapper",
-  "version": "0.8.60",
+  "version": "0.8.62",
   "description": "Generic Mutation Mapper",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
@@ -39,14 +39,15 @@
   },
   "dependencies": {
     "autobind-decorator": "^2.1.0",
-    "cbioportal-frontend-commons": "^0.5.35",
-    "cbioportal-utils": "^0.3.25",
+    "cbioportal-frontend-commons": "^0.5.36",
+    "cbioportal-utils": "^0.3.26",
     "classnames": "^2.2.5",
     "genome-nexus-ts-api-client": "^1.1.23",
     "jquery": "^3.2.1",
     "lodash": "^4.17.15",
     "memoize-weak-decorator": "^1.0.3",
     "mobxpromise": "github:cbioportal/mobxpromise#303db72588860bff0a6862a4f07a4e8a3578c94f",
+    "oncokb-frontend-commons": "^0.0.2",
     "oncokb-styles": "~1.4.2",
     "oncokb-ts-api-client": "^1.3.3",
     "react-collapse": "^4.0.3",
@@ -59,5 +60,5 @@
     "superagent": "^3.8.3",
     "typescript": "4.0.3"
   },
-  "gitHead": "0266028e5d413311483debf29069351bec9c7185"
+  "gitHead": "63d382d8e0dc43706fab10b5812ded0c96ab53b7"
 }

package/dist/component/oncokb/ArticleAbstractItem.d.ts

@@ -1,5 +0,0 @@
-import * as React from 'react';
-import { ArticleAbstract } from 'oncokb-ts-api-client';
-export default class ArticleAbstractItem extends React.Component<ArticleAbstract> {
-    render(): JSX.Element;
-}

package/dist/component/oncokb/OncoKB.d.ts

@@ -1,33 +0,0 @@
-import { MobxCache, OncoKbCardDataType } from 'cbioportal-utils';
-import { IndicatorQueryResp } from 'oncokb-ts-api-client';
-import * as React from 'react';
-import './oncokb.scss';
-import 'oncokb-styles/dist/oncokb.css';
-export interface IOncoKbProps {
-    status: 'pending' | 'error' | 'complete';
-    indicator?: IndicatorQueryResp;
-    availableDataTypes?: OncoKbCardDataType[];
-    mergeAnnotationIcons?: boolean;
-    pubMedCache?: MobxCache;
-    usingPublicOncoKbInstance: boolean;
-    isCancerGene: boolean;
-    geneNotExist: boolean;
-    hugoGeneSymbol: string;
-    userEmailAddress?: string;
-    disableFeedback?: boolean;
-    contentPadding?: number;
-}
-export declare function sortValue(indicator?: IndicatorQueryResp | undefined | null): number[];
-export declare function download(indicator?: IndicatorQueryResp | undefined | null): string;
-export default class OncoKB extends React.Component<IOncoKbProps, {}> {
-    constructor(props: IOncoKbProps);
-    showFeedback: boolean;
-    tooltipDataLoadComplete: boolean;
-    render(): JSX.Element;
-    private multiAnnotationIcon;
-    private levelIcons;
-    private singleAnnotationIcon;
-    private tooltipContent;
-    private handleFeedbackOpen;
-    private handleFeedbackClose;
-}

package/dist/component/oncokb/OncoKB.spec.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/component/oncokb/OncoKBSuggestAnnotationLinkout.d.ts

@@ -1,6 +0,0 @@
-import * as React from 'react';
-export default class OncoKBSuggestAnnotationLinkout extends React.Component<{
-    gene: string;
-}> {
-    render(): JSX.Element;
-}

package/dist/component/oncokb/OncoKbCard.d.ts

@@ -1,20 +0,0 @@
-import { IndicatorQueryResp } from 'oncokb-ts-api-client';
-import * as React from 'react';
-import { ICache } from '../../model/SimpleCache';
-import { OncoKbCardDataType } from 'cbioportal-utils';
-export declare type OncoKbCardProps = {
-    type: OncoKbCardDataType;
-    hugoSymbol: string;
-    geneNotExist: boolean;
-    isCancerGene: boolean;
-    usingPublicOncoKbInstance: boolean;
-    pmidData: ICache;
-    indicator?: IndicatorQueryResp;
-    displayHighestLevelInTabTitle?: boolean;
-    handleFeedbackOpen?: React.EventHandler<any>;
-};
-export default class OncoKbCard extends React.Component<OncoKbCardProps> {
-    constructor(props: any);
-    get oncokbLinkOut(): string | undefined;
-    render(): JSX.Element;
-}

package/dist/component/oncokb/OncoKbCardBody.d.ts

@@ -1,15 +0,0 @@
-import React from 'react';
-import { IndicatorQueryResp } from 'oncokb-ts-api-client';
-import { OncoKbCardDataType } from 'cbioportal-utils';
-import { ICache } from '../../model/SimpleCache';
-export declare type OncoKbCardBodyProps = {
-    type: OncoKbCardDataType;
-    geneNotExist: boolean;
-    isCancerGene: boolean;
-    hugoSymbol: string;
-    pmidData: ICache;
-    indicator?: IndicatorQueryResp;
-    usingPublicOncoKbInstance: boolean;
-    displayHighestLevelInTabTitle?: boolean;
-};
-export declare const OncoKbCardBody: React.FunctionComponent<OncoKbCardBodyProps>;

package/dist/component/oncokb/OncoKbCardLevelsOfEvidenceDropdown.d.ts

@@ -1,15 +0,0 @@
-import React from 'react';
-export declare type LevelsOfEvidenceDropdownProps = {
-    levels: string[];
-    levelDes: {
-        [level: string]: JSX.Element;
-    };
-};
-export default class OncoKbCardLevelsOfEvidenceDropdown extends React.Component<LevelsOfEvidenceDropdownProps> {
-    constructor(props: any);
-    levelsCollapsed: boolean;
-    levelListItem(level: string, levelDes: JSX.Element): JSX.Element;
-    generateLevelRows(): JSX.Element[];
-    handleLevelCollapse(): void;
-    render(): JSX.Element;
-}

package/dist/component/oncokb/OncoKbCardTitle.d.ts

@@ -1,8 +0,0 @@
-import * as React from 'react';
-declare type OncoKbCardDefaultTitleProps = {
-    hugoSymbol: string;
-    variant: string;
-    tumorType: string;
-};
-export declare const OncoKbCardTitle: React.FunctionComponent<OncoKbCardDefaultTitleProps>;
-export {};

package/dist/component/oncokb/OncoKbFeedback.d.ts

@@ -1,12 +0,0 @@
-import * as React from 'react';
-interface IOncoKbFeedbackProps {
-    showFeedback: boolean;
-    hugoSymbol?: string;
-    alteration?: string;
-    userEmailAddress?: string;
-    handleFeedbackClose: () => void;
-}
-export default class OncoKbFeedback extends React.Component<IOncoKbFeedbackProps, {}> {
-    render(): JSX.Element;
-}
-export {};

package/dist/component/oncokb/OncoKbHelper.d.ts

@@ -1,33 +0,0 @@
-import { OncoKbCardDataType } from 'cbioportal-utils';
-export default class OncoKbHelper {
-    static get TX_LEVELS(): string[];
-    static get DX_LEVELS(): string[];
-    static get PX_LEVELS(): string[];
-    static get LEVELS(): string[];
-    static getLevelsDesc(dataType: OncoKbCardDataType): Pick<{
-        [level: string]: JSX.Element;
-    }, string>;
-    static get LEVEL_DESC(): {
-        [level: string]: JSX.Element;
-    };
-    static getDefaultColumnDefinition(columnKey: 'level' | 'alterations'): {
-        id: string;
-        Header: JSX.Element;
-        accessor: string;
-        maxWidth: number;
-        sortMethod: (a: string, b: string) => number;
-        Cell: (props: {
-            value: string;
-        }) => JSX.Element;
-        minWidth?: undefined;
-    } | {
-        id: string;
-        Header: JSX.Element;
-        accessor: string;
-        minWidth: number;
-        sortMethod: (a: string[], b: string[]) => number;
-        maxWidth?: undefined;
-        Cell?: undefined;
-    };
-    static getAlterationsColumnCell: (alterations: string[], variant: string) => JSX.Element;
-}

package/dist/component/oncokb/OncoKbSummaryTable.d.ts

@@ -1,31 +0,0 @@
-import * as React from 'react';
-import { Column } from 'react-table';
-export declare type OncoKbSummaryTableProps = {
-    usingPublicOncoKbInstance: boolean;
-    data: OncoKbSummary[];
-    initialSortColumn?: string;
-    initialSortDirection?: 'asc' | 'desc';
-    initialItemsPerPage?: number;
-};
-export declare type OncoKbSummary = {
-    count: number;
-    proteinChange: string;
-    clinicalImplication: string[];
-    biologicalEffect: string[];
-    level: {
-        level: string;
-        tumorTypes: string[];
-    }[];
-};
-export default class OncoKbSummaryTable extends React.Component<OncoKbSummaryTableProps, {}> {
-    static defaultProps: {
-        data: never[];
-        initialSortColumn: string;
-        initialSortDirection: string;
-        initialItemsPerPage: number;
-    };
-    constructor(props: OncoKbSummaryTableProps);
-    get hasLevelData(): boolean;
-    get columns(): Column[];
-    render(): JSX.Element;
-}

package/dist/component/oncokb/OncoKbTooltip.d.ts

@@ -1,21 +0,0 @@
-import { ICache } from 'cbioportal-frontend-commons';
-import { MobxCache, OncoKbCardDataType } from 'cbioportal-utils';
-import { IndicatorQueryResp } from 'oncokb-ts-api-client';
-import * as React from 'react';
-export interface IOncoKbTooltipProps {
-    type: OncoKbCardDataType;
-    indicator?: IndicatorQueryResp;
-    pubMedCache?: MobxCache;
-    handleFeedbackOpen?: () => void;
-    hugoSymbol: string;
-    isCancerGene: boolean;
-    geneNotExist: boolean;
-    usingPublicOncoKbInstance: boolean;
-}
-/**
- * @author Selcuk Onur Sumer
- */
-export default class OncoKbTooltip extends React.Component<IOncoKbTooltipProps, {}> {
-    get pmidData(): ICache<any>;
-    render(): JSX.Element;
-}

package/dist/component/oncokb/OncoKbTreatmentTable.d.ts

@@ -1,86 +0,0 @@
-import { ICache } from 'cbioportal-frontend-commons';
-import { ArticleAbstract, IndicatorQueryTreatment } from 'oncokb-ts-api-client';
-import * as React from 'react';
-import './oncoKbTreatmentTable.scss';
-declare type OncoKbTreatmentTableProps = {
-    variant: string;
-    treatments: IndicatorQueryTreatment[];
-    pmidData: ICache<any>;
-};
-export default class OncoKbTreatmentTable extends React.Component<OncoKbTreatmentTableProps> {
-    levelTooltipContent: (level: string) => JSX.Element;
-    treatmentTooltipContent: (abstracts: ArticleAbstract[], pmids: number[], pmidData: ICache<any>, description?: string | undefined) => JSX.Element | (() => JSX.Element);
-    readonly columns: ({
-        id: string;
-        Header: JSX.Element;
-        accessor: string;
-        maxWidth: number;
-        sortMethod: (a: string, b: string) => number;
-        Cell: (props: {
-            value: string;
-        }) => JSX.Element;
-        minWidth?: undefined;
-    } | {
-        id: string;
-        Header: JSX.Element;
-        accessor: string;
-        minWidth: number;
-        sortMethod: (a: string[], b: string[]) => number;
-        maxWidth?: undefined;
-        Cell?: undefined;
-    } | {
-        Cell: (props: {
-            value: string[];
-        }) => JSX.Element;
-        id: string;
-        Header: JSX.Element;
-        accessor: string;
-        maxWidth: number;
-        sortMethod: (a: string, b: string) => number;
-        minWidth?: undefined;
-        sortable?: undefined;
-    } | {
-        Cell: (props: {
-            value: string[];
-        }) => JSX.Element;
-        id: string;
-        Header: JSX.Element;
-        accessor: string;
-        minWidth: number;
-        sortMethod: (a: string[], b: string[]) => number;
-        maxWidth?: undefined;
-        sortable?: undefined;
-    } | {
-        id: string;
-        Header: JSX.Element;
-        accessor: string;
-        Cell: (props: {
-            original: IndicatorQueryTreatment;
-        }) => JSX.Element;
-        minWidth?: undefined;
-        sortable?: undefined;
-        maxWidth?: undefined;
-    } | {
-        id: string;
-        Header: JSX.Element;
-        accessor: string;
-        minWidth: number;
-        Cell: (props: {
-            original: IndicatorQueryTreatment;
-        }) => JSX.Element;
-        sortable?: undefined;
-        maxWidth?: undefined;
-    } | {
-        id: string;
-        Header: JSX.Element;
-        sortable: boolean;
-        maxWidth: number;
-        Cell: (props: {
-            original: IndicatorQueryTreatment;
-        }) => false | JSX.Element;
-        accessor?: undefined;
-        minWidth?: undefined;
-    })[];
-    render(): JSX.Element;
-}
-export {};

package/dist/component/oncokb/PmidItem.d.ts

@@ -1,12 +0,0 @@
-import * as React from 'react';
-declare type PmidItemProps = {
-    title: string;
-    author: string;
-    source: string;
-    date: string;
-    pmid: string;
-};
-export default class PmidItem extends React.Component<PmidItemProps> {
-    render(): JSX.Element;
-}
-export {};

package/dist/component/oncokb/RefComponent.d.ts

@@ -1,9 +0,0 @@
-import { ICache } from 'cbioportal-frontend-commons';
-import * as React from 'react';
-export default class RefComponent extends React.Component<{
-    content: string;
-    componentType: 'tooltip' | 'linkout';
-    pmidData: ICache<any>;
-}> {
-    render(): JSX.Element;
-}

package/dist/component/oncokb/ReferenceList.d.ts

@@ -1,13 +0,0 @@
-import { ICache } from 'cbioportal-frontend-commons';
-import { ArticleAbstract } from 'oncokb-ts-api-client';
-import * as React from 'react';
-declare type ReferenceListProps = {
-    pmids: number[];
-    pmidData?: ICache<any>;
-    abstracts: ArticleAbstract[];
-};
-export default class ReferenceList extends React.Component<ReferenceListProps> {
-    get isLoading(): boolean;
-    render(): JSX.Element;
-}
-export {};

package/dist/component/oncokb/SummaryWithRefs.d.ts

@@ -1,11 +0,0 @@
-import { ICache } from 'cbioportal-frontend-commons';
-import * as React from 'react';
-declare type SummaryWithRefsProps = {
-    content: string | undefined;
-    type: 'tooltip' | 'linkout';
-    pmidData: ICache<any>;
-};
-export default class SummaryWithRefs extends React.Component<SummaryWithRefsProps> {
-    render(): JSX.Element;
-}
-export {};

package/dist/component/oncokb/constants.d.ts

@@ -1,10 +0,0 @@
-export declare enum OtherBiomarkersQueryType {
-    MSIH = "MSIH",
-    TMBH = "TMBI"
-}
-export declare const OTHER_BIOMARKER_HUGO_SYMBOL = "Other Biomarkers";
-export declare const MSI_H_NAME = "MSI-H";
-export declare const TMB_H_NAME = "TMB-H";
-export declare const OTHER_BIOMARKER_NAME: {
-    [key in OtherBiomarkersQueryType]: string;
-};

package/dist/component/oncokb/icon/AnnotationIcon.d.ts

@@ -1,13 +0,0 @@
-import React from 'react';
-import { OncoKbCardDataType } from 'cbioportal-utils';
-import { IndicatorQueryResp } from 'oncokb-ts-api-client';
-export declare const AnnotationIcon: React.FunctionComponent<{
-    type: OncoKbCardDataType;
-    tooltipOverlay?: JSX.Element;
-    indicator?: IndicatorQueryResp;
-    availableDataTypes?: OncoKbCardDataType[];
-}>;
-export declare const AnnotationIconWithTooltip: React.FunctionComponent<{
-    tooltipOverlay?: JSX.Element;
-    icon?: JSX.Element;
-}>;

package/dist/component/oncokb/icon/CompactAnnotationIcon.d.ts

@@ -1,8 +0,0 @@
-import React from 'react';
-import { OncoKbCardDataType } from 'cbioportal-utils';
-import { IndicatorQueryResp } from 'oncokb-ts-api-client';
-export declare const CompactAnnotationIcon: React.FunctionComponent<{
-    usingPublicOncoKbInstance: boolean;
-    indicator?: IndicatorQueryResp;
-    availableDataTypes?: OncoKbCardDataType[];
-}>;

package/dist/component/oncokb/icon/LevelIcon.d.ts

@@ -1,6 +0,0 @@
-import * as React from 'react';
-declare const LevelIcon: React.FunctionComponent<{
-    level: string;
-    showDescription?: boolean;
-}>;
-export default LevelIcon;

package/dist/component/oncokb/icon/OncogenicIcon.d.ts

@@ -1,6 +0,0 @@
-import * as React from 'react';
-declare const OncogenicIcon: React.FunctionComponent<{
-    oncogenicity: string;
-    showDescription?: boolean;
-}>;
-export default OncogenicIcon;