Merge stable version for Cbioportal

iVis-at-Bilkent · Jan 12, 2021 · 36c2c6c · 36c2c6c
2 parents ca4b9c7 + 921401e
commit 36c2c6c
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diff --git a/README.md b/README.md
@@ -5,6 +5,11 @@ PathwayMapper is a web based pathway curation tool for interactive creation, edi
   <img src="assets/sample-screenshot.png" width="600"/>
 </p>
 
+A special, viewer edition of PathwayMapper was built for use in cBioPortal ([example](https://www.cbioportal.org/results/pathways?Action=Submit&Z_SCORE_THRESHOLD=1.0&cancer_study_id=gbm_tcga_pub&cancer_study_list=gbm_tcga_pub&case_set_id=gbm_tcga_pub_sequenced&gene_list=TP53%20MDM2%20MDM4&gene_set_choice=user-defined_list&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=gbm_tcga_pub_cna_rae&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=gbm_tcga_pub_mutations), [tutorial](https://www.cbioportal.org/tutorials)).
+<p align="center">
+  <img src="assets/sample-screenshot-cBioPortal.png" width="600"/>
+</p>
+
 Below is a video tutorial on basics of PathwayMapper:
 <a href="https://youtu.be/jvEueUqZZPI" target="_blank"><p align="center"><img src="assets/basics-of-PM.jpg" width="340" title="Click to watch video"/></p></a>
 
@@ -260,7 +265,7 @@ Icons made by [Freepik](http://www.freepik.com),
 
 ## Team
 
-  * [Ziya Erkoc](https://github.com/Rgtemze), [Ugur Dogrusoz](https://github.com/ugurdogrusoz) of [i-Vis at Bilkent University](http://www.cs.bilkent.edu.tr/~ivis), [Ozgun Babur](https://github.com/ozgunbabur) of OHSU, and Konnor C. La, [Jianjiong Gao](https://github.com/jjgao), Nikolaus Schultz of [The Nikolaus Schultz lab at MSKCC](https://www.mskcc.org/research-areas/labs/nikolaus-schultz).
+  * [Ziya Erkoc](https://github.com/Rgtemze), [Ugur Dogrusoz](https://github.com/ugurdogrusoz) of [i-Vis at Bilkent University](http://www.cs.bilkent.edu.tr/~ivis), [Ozgun Babur](https://github.com/ozgunbabur) of OHSU, and [S. Onur Sumer](https://github.com/onursumer), Konnor C. La, [Jianjiong Gao](https://github.com/jjgao), Nikolaus Schultz of [The Nikolaus Schultz lab at MSKCC](https://www.mskcc.org/research-areas/labs/nikolaus-schultz).
 
 #### Alumni
 

diff --git a/assets/sample-screenshot-cBioPortal.png b/assets/sample-screenshot-cBioPortal.png
diff --git a/dist/index.html b/dist/index.html
@@ -11,12 +11,12 @@
   <!-- TODO this is a quick fix for the excluded 3rd party css dependencies, it is probably not a good idea to have direct references to github cdn -->
   <link rel="stylesheet" href="https://cdn.rawgit.com/cytoscape/cytoscape.js-panzoom/master/cytoscape.js-panzoom.css">
   <link rel="stylesheet" href="https://cdn.rawgit.com/cytoscape/cytoscape.js-navigator/master/cytoscape.js-navigator.css">
-<link href="./base.css?96ffa502a2d64c3c1fe4" rel="stylesheet"></head>
+<link href="./base.css?6d5c79b49d0b53c6b522" rel="stylesheet"></head>
 
 <body class="pathwayMapper">
   <div>
     <div id="app"></div>
   </div>
-<script type="text/javascript" src="react-pathway-mapper.es5.js?96ffa502a2d64c3c1fe4"></script></body>
+<script type="text/javascript" src="react-pathway-mapper.es5.js?6d5c79b49d0b53c6b522"></script></body>
 
 </html>
diff --git a/dist/managers/EditorActionsManager.d.ts b/dist/managers/EditorActionsManager.d.ts
@@ -121,6 +121,7 @@ export default class EditorActionsManager {
     updateVisibility(ele: any, isHidden: boolean): void;
     updateElementCallback(op: any): void;
     getGenomicDataSVG(node: any): any;
+    getOncoprintDataSVG(node: any): any;
     removeGenomicData(): void;
     addGenomicData(genomicData: any): void;
     adjustVisibilityShareDB(profileId: string, isEnabled: boolean): void;

diff --git a/dist/managers/FileOperationsManager.d.ts b/dist/managers/FileOperationsManager.d.ts
@@ -7,7 +7,7 @@ export interface IPathwayInfo {
 export default class FileOperationsManager {
     pathwayInfo: IPathwayInfo;
     constructor();
-    readonly getPathwayInfo: IPathwayInfo;
+    get getPathwayInfo(): IPathwayInfo;
     setPathwayInfo(other: IPathwayInfo): void;
     b64toBlob(b64Data: any, contentType: any, sliceSize?: number): Blob;
     saveAsJPEG(cy: any): void;

diff --git a/dist/managers/GenomicDataOverlayManager.d.ts b/dist/managers/GenomicDataOverlayManager.d.ts
@@ -1,8 +1,10 @@
+/// <reference types="jquery" />
 export default class GenomicDataOverlayManager {
     genomicDataMap: {};
     visibleGenomicDataMapByType: {};
     groupedGenomicDataCount: number;
     groupedGenomicDataMap: {};
+    patientData: any;
     private DEFAULT_VISIBLE_GENOMIC_DATA_COUNT;
     private MAX_VISIBLE_GENOMIC_DATA_COUNT;
     private observers;
@@ -36,4 +38,12 @@ export default class GenomicDataOverlayManager {
     parseGenomicData(genomicData: any, groupID: any): void;
     registerObserver(observer: any): void;
     notifyObservers(): void;
+    getAlterationCountForPatient(geneData: any): number;
+    showPatientData(): void;
+    getOncoprintColors(selectedGene: any): any;
+    generateSVGForPatientNode(ele: any, patientData: any): any;
+    generateOncoprintForPatientNode(ele: any): any;
+    getCNADisplayString(alterationTypeKey: number): string;
+    generateSvgIconForSample(iconColor: string, iconText: string): string;
+    generateHTMLContentForNodeTooltip(ele: any, patientData: any): JQuery<HTMLElement>;
 }
diff --git a/dist/managers/QtipManager.d.ts b/dist/managers/QtipManager.d.ts
@@ -1,3 +1,4 @@
+/// <reference types="jquery" />
 import EditorActionsManager from "./EditorActionsManager";
 export default class QtipManager {
     private cy;

diff --git a/dist/modals/CBioHelpModal.d.ts b/dist/modals/CBioHelpModal.d.ts
@@ -3,9 +3,11 @@ import { EModalType } from '../ui/react-pathway-mapper';
 interface ICBioHelpModalProps {
     isModalShown: boolean;
     handleClose: (modalId: EModalType) => void;
+    patientView?: boolean;
 }
 export default class CBioHelpModal extends React.Component<ICBioHelpModalProps> {
     constructor(props: ICBioHelpModalProps);
+    generateOncoprintLegend(): SVGSVGElement;
     render(): JSX.Element;
 }
 export {};
diff --git a/dist/modals/ProfilesModal.d.ts b/dist/modals/ProfilesModal.d.ts
@@ -9,7 +9,7 @@ interface IProfilesModalProps {
 }
 export default class ProfilesModal extends React.Component<IProfilesModalProps, {}> {
     constructor(props: IProfilesModalProps);
-    readonly profileEnabledMap: {};
+    get profileEnabledMap(): {};
     render(): JSX.Element;
 }
 export {};
diff --git a/dist/react-pathway-mapper.es5.js b/dist/react-pathway-mapper.es5.js
diff --git a/dist/react-pathway-mapper.es5.js.map b/dist/react-pathway-mapper.es5.js.map
diff --git a/dist/ui/Ranking.d.ts b/dist/ui/Ranking.d.ts
@@ -5,6 +5,7 @@ interface IRankingProps {
     pathwayActions: PathwayActions;
     bestPathwaysAlgos: any[][];
     tableComponent: (data: IPathwayMapperTable[], selectedPathway: string, onPathwaySelect: (pathway: string) => void) => JSX.Element;
+    patientView?: boolean;
 }
 export default class Ranking extends React.Component<IRankingProps, {}> {
     bestPathways: any[];
@@ -14,7 +15,7 @@ export default class Ranking extends React.Component<IRankingProps, {}> {
     isAlterationEnabled: number;
     isExpanded: boolean;
     readonly COUNT_PERC_EXPLANATION = "Whether we should favor the number of genes of interest matching the ones in a pathway or the percentage of such genes in that pathway. For instance, suppose genes of interest are A, B, and C, and the pathway contains genes B, C, D, and E. When we consider count, the score is 2 (for the two genes that match). However, when we consider percentage the score will be 50% as 2 of the 4 genes in the pathway are among genes of interest.";
-    readonly ALTERATION_EXPLANATION = "When this is checked, each matching gene will not directly contribute to the score as 1 unit but with the alteration frequency percentage of that gene. For instance, suppose genes of interest are A, B, and C with alteration frequencies of 0.5, 0.2, and 0.3, respectively, and the pathway contains genes B, C, D, and E. When this is option isn't checked, the score will be 2 for match count and %50 for the match percentage. However, when this option is checked, the scores will be 0.2+0.3=0.5 and (0.2+0.3)/4=%12.5 for match count and percentage, respectively.";
+    readonly ALTERATION_EXPLANATION = "When this is checked, each matching gene will not directly contribute to the score as 1 unit but with the alteration frequency percentage of that gene. For instance, suppose genes of interest are A, B, and C with alteration frequencies of 0.5, 0.2, and 0.3, respectively, and the pathway contains genes B, C, D, and E. When this is option isn't checked, the score will be 2 for match count and 50% for the match percentage. However, when this option is checked, the scores will be 0.2+0.3=0.5 and (0.2+0.3)/4=12.5% for match count and percentage, respectively.";
     constructor(props: IRankingProps);
     setBestPathwayMethod(i: number): void;
     onPathwayClick(pathway: string): void;

diff --git a/dist/ui/Toolbar.d.ts b/dist/ui/Toolbar.d.ts
@@ -8,9 +8,10 @@ interface IToolbarProps {
     handleOpen: (modalId: number) => void;
     genes: any[];
     validGenes: any;
-    toast: any;
+    showMessage: (message: string) => void;
     pathwayGenes: string[];
     onAddGenes: (selectedGenes: string[]) => void;
+    patientView?: boolean;
 }
 export default class Toolbar extends React.Component<IToolbarProps, {}> {
     selectedGenes: string[];

diff --git a/dist/ui/react-pathway-mapper.d.ts b/dist/ui/react-pathway-mapper.d.ts
@@ -3,6 +3,7 @@ import EditorActionsManager from "../managers/EditorActionsManager";
 import FileOperationsManager from '../managers/FileOperationsManager';
 import PathwayActions from '../utils/PathwayActions';
 import CBioPortalAccessor from '../utils/CBioPortalAccessor';
+import { IGeneticAlterationRuleSetParams } from 'oncoprintjs';
 import ViewOperationsManager from '../managers/ViewOperationsManager';
 import GridOptionsManager from '../managers/GridOptionsManager';
 import "../css/pmv1.css";
@@ -13,6 +14,7 @@ interface IPathwayMapperProps {
     genes: any[];
     isCollaborative?: boolean;
     cBioAlterationData?: ICBioData[];
+    sampleIconData?: ISampleIconData;
     pathwayName?: string;
     alterationData?: IAlterationData;
     onAddGenes?: (selectedGenes: string[]) => void;
@@ -21,12 +23,25 @@ interface IPathwayMapperProps {
     tableComponent?: (data: IPathwayMapperTable[], selectedPathway: string, onPathwaySelect: (pathway: string) => void) => JSX.Element;
     validGenes?: any;
     toast: any;
+    showMessage: (message: string) => void;
+    patientView?: boolean;
+    messageBanner?: () => JSX.Element;
 }
 export interface ICBioData {
     altered: number;
     gene: string;
     percentAltered: string;
     sequenced: number;
+    geneticTrackData?: any[];
+    geneticTrackRuleSetParams?: IGeneticAlterationRuleSetParams;
+}
+export interface ISampleIconData {
+    sampleIndex: {
+        [s: string]: number;
+    };
+    sampleColors: {
+        [s: string]: string;
+    };
 }
 export declare enum EModalType {
     STUDY = 0,
@@ -75,6 +90,7 @@ export default class PathwayMapper extends React.Component<IPathwayMapperProps,
     isModalShown: boolean[];
     portalAcessor: CBioPortalAccessor;
     alterationData: IAlterationData;
+    patientData: any[][];
     pathwayGeneMap: {
         [key: string]: {
             [key: string]: string;
@@ -87,7 +103,11 @@ export default class PathwayMapper extends React.Component<IPathwayMapperProps,
     viewOperationsManager: ViewOperationsManager;
     gridOptionsManager: GridOptionsManager;
     constructor(props: IPathwayMapperProps);
+    setSelectedPathway(pathway: string): void;
+    setEditor(editor: EditorActionsManager): void;
     calculateAlterationData(cBioAlterationData: ICBioData[]): void;
+    calculatePatientData(cBioAlterationData: ICBioData[]): void;
+    addSampleIconData(sampleIconData: any): void;
     getGeneStudyMap(studyGeneMap: any): any;
     getAlterationAveragePerGene(genomicDataMap: any): any;
     /**
@@ -99,7 +119,7 @@ export default class PathwayMapper extends React.Component<IPathwayMapperProps,
     includePathway(pathwayData?: IPathwayData, pathwayName?: string): void;
     extractAllGenes(): void;
     loadRedirectedPortalData(): void;
-    readonly profileEnabledMap: {};
+    get profileEnabledMap(): {};
     doesProfileExist(profileId: string): boolean;
     loadFromCBio(dataTypes: {
         [dataType: string]: IDataTypeMetaData;

diff --git a/dist/utils/PathwayActions.d.ts b/dist/utils/PathwayActions.d.ts
@@ -39,7 +39,7 @@ export default class PathwayActions {
     merge(): void;
     setOverlayUploader(inputRef: any): void;
     setUploaders(inputRef: any, isMerge: boolean): void;
-    readonly getPathwayInfo: IPathwayInfo;
+    get getPathwayInfo(): IPathwayInfo;
     setPathwayInfo(other: IPathwayInfo): void;
     undo(): void;
     redo(): void;

diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "pathway-mapper",
-  "version": "2.0.1",
+  "version": "2.0.3",
   "description": "",
   "keywords": [],
   "main": "dist/react-pathway-mapper.es5.js",
@@ -62,8 +62,8 @@
   "peerDependencies": {
     "bootstrap": "^3.0.0 || ^4.0.0",
     "jquery": "^1.4 || ^2.0 || ^3.0",
-    "mobx": "^3.0.0 || ^4.0.0 || ^5.0.0",
-    "mobx-react": "^4.0.0 || ^5.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^6.0.0",
     "react": "^15.0.0 || ^16.0.0",
     "react-bootstrap": "^0.30.0",
     "react-dom": "^15.0.0 || ^16.0.0"
@@ -86,6 +86,7 @@
     "file-saver": "^2.0.2",
     "jquery-ui-dist": "^1.12.1",
     "konva": "^1.6.3",
+    "oncoprintjs": "4.2.3",
     "react-loader-spinner": "^2.3.0",
     "react-scrollbar": "^0.5.6",
     "react-table": "^6.10.0",
@@ -126,8 +127,8 @@
     "jquery": "latest",
     "lint-staged": "^8.0.0",
     "lodash.camelcase": "^4.3.0",
-    "mobx": "^5.10.1",
-    "mobx-react": "^5.4.3",
+    "mobx": "^6.0.0",
+    "mobx-react": "^6.0.0",
     "multer": "^1.4.1",
     "prettier": "^1.14.3",
     "prompt": "^1.0.0",
@@ -150,7 +151,7 @@
     "tslint-config-standard": "^8.0.1",
     "ttf-loader": "^1.0.2",
     "typedoc": "^0.12.0",
-    "typescript": "3.2.2",
+    "typescript": "4.1.3",
     "sharedb-mongo": "latest",
     "websocket-json-stream": "0.0.3",
     "ws": "latest",

diff --git a/src/images/toolbar/PatientViewHelp.png b/src/images/toolbar/PatientViewHelp.png
diff --git a/src/managers/EditorActionsManager.tsx b/src/managers/EditorActionsManager.tsx
@@ -3,7 +3,7 @@ import CBioPortalAccessor from "../utils/CBioPortalAccessor";
 import SVGExporter from "../utils/SVGExporter";
 import GenomicDataOverlayManager from "./GenomicDataOverlayManager";
 import { IProfileMetaData, IPathwayData } from "../ui/react-pathway-mapper";
-import { observable } from "mobx";
+import { observable, makeObservable } from "mobx";
 import LayoutProperties, { ILayoutProperties } from "../modals/LayoutProperties";
 
 const _ = require('underscore');
@@ -61,6 +61,7 @@ export default class EditorActionsManager{
                 undoRedoManager: any, portalAccessor: CBioPortalAccessor, profiles: IProfileMetaData[])
     {
         // Set cy instance and set real time manager reference if collaborative mode
+        makeObservable(this);
         this.cy = cyInst;
         this.isCollaborative = isCollaborative;
         this.isCbioPortal = isCBioPortal;
@@ -1676,6 +1677,11 @@ export default class EditorActionsManager{
         return this.genomicDataOverlayManager.generateSVGForNode(node);
     }
 
+    getOncoprintDataSVG(node: any) 
+    {
+        return this.genomicDataOverlayManager.generateOncoprintForPatientNode(node);
+    }
+
     removeGenomicData()
     {
         if(this.isCollaborative)

diff --git a/src/managers/FileOperationsManager.tsx b/src/managers/FileOperationsManager.tsx
@@ -1,7 +1,7 @@
 import SaveLoadUtilities from '../utils/SaveLoadUtility.js';
 import {saveAs} from 'file-saver';
 import EditorActionsManager from './EditorActionsManager.js';
-import { observable, computed } from 'mobx';
+import { observable, computed, makeObservable } from 'mobx';
 import SaveLoadUtility from '../utils/SaveLoadUtility';
 
 
@@ -18,6 +18,7 @@ export default class FileOperationsManager{
     pathwayInfo: IPathwayInfo;
 
     constructor(){
+        makeObservable(this);
         this.pathwayInfo = {pathwayTitle: "New Pathway", pathwayDetails: "", fileName: "pathway.txt"};
     }