Merge branch 'unstable'

iVis-at-Bilkent · Feb 5, 2021 · 14d5204 · 14d5204
2 parents 7b015c3 + 61c039a
commit 14d5204
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Showing 56 changed files with 11,331 additions and 10,745 deletions.
diff --git a/dist/base.css b/dist/base.css
diff --git a/dist/base.css.map b/dist/base.css.map
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?36673459e7a12c966586" rel="stylesheet"></head>
+<link href="./base.css?993f6ad183eea8f6ecf6" rel="stylesheet"></head>
 
 <body class="pathwayMapper">
   <div>
     <div id="app"></div>
   </div>
-<script type="text/javascript" src="react-pathway-mapper.es5.js?36673459e7a12c966586"></script></body>
+<script type="text/javascript" src="react-pathway-mapper.es5.js?993f6ad183eea8f6ecf6"></script></body>
 
 </html>
diff --git a/dist/managers/ContextMenuManager.d.ts b/dist/managers/ContextMenuManager.d.ts
@@ -1,13 +1,12 @@
-import EditorActionsManager from "./EditorActionsManager";
 import { EModalType } from "../ui/react-pathway-mapper";
+import EditorActionsManager from "./EditorActionsManager";
 export default class ContextMenuManager {
     private cy;
     private editor;
-    private isCBioPortal;
     private handleOpen;
     private undoRedoManager;
     private isCollaborative;
-    constructor(cy: any, editor: EditorActionsManager, isCBioPortal: boolean, handleOpen: (modalId: EModalType) => void, undoRedoManager: any, isCollaborative: boolean);
+    constructor(cy: any, editor: EditorActionsManager, handleOpen: (modalId: EModalType) => void, undoRedoManager: any, isCollaborative: boolean);
     init(): void;
     isChildren(node: any, queryNode: any): boolean;
 }
diff --git a/dist/managers/EditorActionsManager.d.ts b/dist/managers/EditorActionsManager.d.ts
@@ -1,7 +1,7 @@
+import { ILayoutProperties } from "../modals/LayoutProperties";
+import { IProfileMetaData } from "../ui/react-pathway-mapper";
 import CBioPortalAccessor from "../utils/CBioPortalAccessor";
 import GenomicDataOverlayManager from "./GenomicDataOverlayManager";
-import { IProfileMetaData } from "../ui/react-pathway-mapper";
-import { ILayoutProperties } from "../modals/LayoutProperties";
 export default class EditorActionsManager {
     static defaultLayoutProperties: ILayoutProperties;
     cy: any;
@@ -18,8 +18,10 @@ export default class EditorActionsManager {
     private shareDBManager;
     private portalAccessor;
     private profiles;
-    private modifyPathwayGeneMap;
     constructor(isCollaborative: boolean, shareDBManager: any, cyInst: any, isCBioPortal: boolean, undoRedoManager: any, portalAccessor: CBioPortalAccessor, profiles: IProfileMetaData[]);
+    setProfile(index: number, profile: IProfileMetaData): void;
+    addProfile(profile: IProfileMetaData): void;
+    removeProfiles(): void;
     handleChangePositionByAlignment(movedNodeArr: any): void;
     doChangePosition(movedNodes: any): any[];
     undoChangePosition(movedNodes: any): any[];

diff --git a/dist/managers/GenomicDataOverlayManager.d.ts b/dist/managers/GenomicDataOverlayManager.d.ts
@@ -6,7 +6,6 @@ export default class GenomicDataOverlayManager {
     groupedGenomicDataMap: {};
     patientData: any;
     private DEFAULT_VISIBLE_GENOMIC_DATA_COUNT;
-    private MAX_VISIBLE_GENOMIC_DATA_COUNT;
     private observers;
     private cy;
     constructor(cy: any);

diff --git a/dist/modals/PathwayDetailsModal.d.ts b/dist/modals/PathwayDetailsModal.d.ts
@@ -1,6 +1,6 @@
 import React from 'react';
-import PathwayActions from '../utils/PathwayActions';
 import { IPathwayInfo } from '../managers/FileOperationsManager';
+import PathwayActions from '../utils/PathwayActions';
 interface IPathwayDetailsModalProps {
     isModalShown: boolean;
     handleClose: Function;

diff --git a/dist/modals/ProfilesModal.d.ts b/dist/modals/ProfilesModal.d.ts
@@ -1,15 +1,17 @@
 import React from "react";
-import { IProfileMetaData } from "../ui/react-pathway-mapper";
 import EditorActionsManager from "../managers/EditorActionsManager";
+import { IProfileMetaData } from "../ui/react-pathway-mapper";
 interface IProfilesModalProps {
     profiles: IProfileMetaData[];
     editor: EditorActionsManager;
     isModalShown: boolean;
     handleClose: Function;
+    handleProfileLabelClicked: (index: number) => void;
 }
 export default class ProfilesModal extends React.Component<IProfilesModalProps, {}> {
     constructor(props: IProfilesModalProps);
     get profileEnabledMap(): {};
+    handleProfileLabelClicked(index: number): void;
     render(): JSX.Element;
 }
 export {};
diff --git a/dist/modals/StudyModal.d.ts b/dist/modals/StudyModal.d.ts
@@ -14,11 +14,14 @@ export default class StudyModal extends React.Component<IStudyModalProps, {}> {
     selectedStudyData: any[];
     portalAccessor: CBioPortalAccessor;
     constructor(props: IStudyModalProps);
+    setSelectedStudyData(data: any[]): void;
+    setDataTypeProperties(dataType: string, properties: IDataTypeMetaData): void;
     preparePortalAccess(studyId: string): void;
     disableAllDataTypes(): void;
     fetchStudy(): void;
     resetModal(): void;
     handleCheckboxClick(dataType: any): void;
+    get selectedStudyDataTitle(): any;
     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/Buttonbar.d.ts b/dist/ui/Buttonbar.d.ts
@@ -1,7 +1,7 @@
 import React from "react";
+import { EGridType } from "../modals/GridSettings";
 import PathwayActions from "../utils/PathwayActions";
 import { EModalType } from "./react-pathway-mapper";
-import { EGridType } from "../modals/GridSettings";
 interface IButtonbarProps {
     pathwayActions: PathwayActions;
     handleOpen: (modelId: EModalType) => void;

diff --git a/dist/ui/CytoscapeArea.d.ts b/dist/ui/CytoscapeArea.d.ts
@@ -1,5 +1,5 @@
 import React from 'react';
-import { IProfileMetaData, EModalType } from './react-pathway-mapper';
+import { EModalType, IProfileMetaData } from './react-pathway-mapper';
 declare type PathwayMapperType = {
     isCollaborative: boolean;
     isCbioPortal: boolean;

diff --git a/dist/ui/Ranking.d.ts b/dist/ui/Ranking.d.ts
@@ -9,17 +9,21 @@ interface IRankingProps {
 }
 export default class Ranking extends React.Component<IRankingProps, {}> {
     bestPathways: any[];
+    shownPathways: any[];
     dropDownTitle: string;
     selectedPathway: string;
     isPercentageMatch: number;
     isAlterationEnabled: number;
+    considerOnlyTCGAPanPathways: boolean;
     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 TCGA_PANCAN_EXPLANATION = "The pathways listed above were retrieved from PathwayMapper. When this option is checked, only the pathways under TCGA > PanCanAtlas will be shown. Uncheck to show all.";
     constructor(props: IRankingProps);
     setBestPathwayMethod(i: number): void;
     onPathwayClick(pathway: string): void;
     onApplyClick(): void;
+    toggleConsiderOnlyTCGAPanPathways(): void;
     componentDidMount(): void;
     render(): JSX.Element;
 }

diff --git a/dist/ui/Sidebar.d.ts b/dist/ui/Sidebar.d.ts
@@ -1,6 +1,6 @@
 import React from "react";
-import PathwayActions from "../utils/PathwayActions";
 import "../css/supp.css";
+import PathwayActions from "../utils/PathwayActions";
 interface ISideBarProps {
     pathwayActions: PathwayActions;
     setActiveEdgeHandler: Function;

diff --git a/dist/ui/Toolbar.d.ts b/dist/ui/Toolbar.d.ts
@@ -1,6 +1,6 @@
 import React from 'react';
-import PathwayActions from '../utils/PathwayActions';
 import { IAlterationData } from '../ui/react-pathway-mapper';
+import PathwayActions from '../utils/PathwayActions';
 interface IToolbarProps {
     pathwayActions: PathwayActions;
     selectedPathway: string;

diff --git a/dist/ui/react-pathway-mapper.d.ts b/dist/ui/react-pathway-mapper.d.ts
@@ -1,14 +1,14 @@
-import React from 'react';
-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 React from 'react';
 import "../css/pmv1.css";
 import "../css/pmv2.css";
 import '../css/qtip.css';
+import EditorActionsManager from "../managers/EditorActionsManager";
+import FileOperationsManager from '../managers/FileOperationsManager';
+import GridOptionsManager from '../managers/GridOptionsManager';
+import ViewOperationsManager from '../managers/ViewOperationsManager';
+import CBioPortalAccessor from '../utils/CBioPortalAccessor';
+import PathwayActions from '../utils/PathwayActions';
 interface IPathwayMapperProps {
     isCBioPortal: boolean;
     genes: any[];
@@ -105,6 +105,8 @@ export default class PathwayMapper extends React.Component<IPathwayMapperProps,
     constructor(props: IPathwayMapperProps);
     setSelectedPathway(pathway: string): void;
     setEditor(editor: EditorActionsManager): void;
+    addProfile(profile: IProfileMetaData): void;
+    toggleProfileEnabled(index: number): void;
     calculateAlterationData(cBioAlterationData: ICBioData[]): void;
     calculatePatientData(cBioAlterationData: ICBioData[]): void;
     addSampleIconData(sampleIconData: any): void;

diff --git a/dist/utils/PathwayActions.d.ts b/dist/utils/PathwayActions.d.ts
@@ -1,10 +1,10 @@
-import EditorActionsManager from '../managers/EditorActionsManager';
-import FileOperationsManager, { IPathwayInfo } from '../managers/FileOperationsManager';
-import { IProfileMetaData, EModalType } from '../ui/react-pathway-mapper';
-import ViewOperationsManager from '../managers/ViewOperationsManager';
-import GridOptionsManager from '../managers/GridOptionsManager';
-import { ILayoutProperties } from '../modals/LayoutProperties';
-import { EGridType } from '../modals/GridSettings';
+import EditorActionsManager from "../managers/EditorActionsManager";
+import FileOperationsManager, { IPathwayInfo } from "../managers/FileOperationsManager";
+import GridOptionsManager from "../managers/GridOptionsManager";
+import ViewOperationsManager from "../managers/ViewOperationsManager";
+import { EGridType } from "../modals/GridSettings";
+import { ILayoutProperties } from "../modals/LayoutProperties";
+import { EModalType, IProfileMetaData } from "../ui/react-pathway-mapper";
 export default class PathwayActions {
     selectedPathway: string;
     fileManager: FileOperationsManager;
@@ -23,6 +23,8 @@ export default class PathwayActions {
     overlayUploader: any;
     enabledType: EGridType;
     constructor(pathwayHandler: (pathwayName: string) => void, profiles: IProfileMetaData[], fileManager: FileOperationsManager, handleOpen: (modalId: EModalType) => void, isCBioPortal: boolean, isCollaborative: boolean);
+    addProfile(profile: IProfileMetaData): void;
+    clearProfiles(): void;
     emphasiseQueryGenes(queryGenes: string[]): void;
     getSelectedNodes(): any;
     setLayoutProperties(layoutProperties: ILayoutProperties): void;

diff --git a/legacy_code/bin/base.min.css b/legacy_code/bin/base.min.css
diff --git a/legacy_code/src/css/sass/base.scss b/legacy_code/src/css/sass/base.scss
@@ -171,7 +171,7 @@ input[type="color"]:hover{
   width: 100%;
 
   .form-control{
-    border-radius: 6px !important;
+    border-radius: 6px;
   }
   input[type="checkbox"]{
     margin-top: 10px;

diff --git a/package.json b/package.json
@@ -51,8 +51,8 @@
     }
   },
   "prettier": {
-    "semi": false,
-    "singleQuote": true
+    "semi": true,
+    "singleQuote": false
   },
   "commitlint": {
     "extends": [
@@ -86,14 +86,14 @@
     "file-saver": "^2.0.2",
     "jquery-ui-dist": "^1.12.1",
     "konva": "^1.6.3",
-    "oncoprintjs": "4.2.3",
+    "lodash": "^4.17.11",
+    "oncoprintjs": "^4.2.3",
     "react-loader-spinner": "^2.3.0",
     "react-scrollbar": "^0.5.6",
     "react-table": "^6.10.0",
     "react-toastify": "^5.3.1",
     "react-tooltip": "^3.10.0",
-    "sharedb": "^1.1.0",
-    "underscore": "~1.8.3"
+    "sharedb": "^1.1.0"
   },
   "devDependencies": {
     "@commitlint/cli": "^7.1.2",
@@ -117,7 +117,6 @@
     "cross-env": "^5.2.0",
     "cz-conventional-changelog": "^2.1.0",
     "express": "^4.17.1",
-    "extract-text-webpack-plugin": "^4.0.0-beta.0",
     "file-loader": "^3.0.1",
     "html-webpack-plugin": "^3.2.0",
     "http-server": "^0.11.1",
@@ -127,6 +126,7 @@
     "jquery": "latest",
     "lint-staged": "^8.0.0",
     "lodash.camelcase": "^4.3.0",
+    "mini-css-extract-plugin": "^0.6.0",
     "mobx": "^6.0.0",
     "mobx-react": "^6.0.0",
     "multer": "^1.4.1",
@@ -140,25 +140,25 @@
     "replace-in-file": "^3.4.2",
     "rimraf": "^2.6.2",
     "semantic-release": "^15.9.16",
+    "sharedb-mongo": "latest",
     "shelljs": "^0.8.3",
     "source-map-loader": "^0.1.6",
     "travis-deploy-once": "^5.0.9",
-    "ts-loader": "4.0.0",
     "ts-jest": "^23.10.2",
+    "ts-loader": "4.0.0",
     "ts-node": "^7.0.1",
     "tslint": "^5.11.0",
     "tslint-config-prettier": "^1.15.0",
     "tslint-config-standard": "^8.0.1",
     "ttf-loader": "^1.0.2",
     "typedoc": "^0.12.0",
     "typescript": "4.1.3",
-    "sharedb-mongo": "latest",
-    "websocket-json-stream": "0.0.3",
-    "ws": "latest",
     "url-loader": "^1.1.2",
     "webpack": "^4.32.2",
     "webpack-cli": "^3.3.2",
     "webpack-dev-server": "^3.5.1",
-    "webpack-node-externals": "^1.7.2"
+    "webpack-node-externals": "^1.7.2",
+    "websocket-json-stream": "0.0.3",
+    "ws": "latest"
   }
 }
diff --git a/src/css/pmv1.css b/src/css/pmv1.css
diff --git a/src/css/pmv2.css b/src/css/pmv2.css
diff --git a/src/css/supp.css b/src/css/supp.css
@@ -179,3 +179,7 @@ transform: scale(0.86);
 .pathwayMapper .smallToast {
     width: 325px;
 }
+
+.pathwayMapper #search-gene-input-group-addon:hover {
+    background-color: #fff;
+}
diff --git a/src/index.jsx b/src/index.jsx
@@ -5,7 +5,6 @@ import WelcomePage from "./ui/WelcomePage";
 
 window.onload = () => {
   const rootEl = document.getElementById('app');
-  console.log(window.location.search);
   const placeHolderGenes = [/*{hugoGeneSymbol: "TP53"}, {hugoGeneSymbol: "CDKN2A"}, {hugoGeneSymbol: "CCNE1"}, {hugoGeneSymbol: "MDM4"}*/];
 
 
@@ -20,8 +19,6 @@ window.onload = () => {
     genes = genesParam.split("+").map(gene => ({hugoGeneSymbol: gene}))
   }
 
-  console.log(genes);
-
   const id = findGetParameter("id");
 
   if(!id){

diff --git a/src/managers/ContextMenuManager.tsx b/src/managers/ContextMenuManager.tsx
@@ -1,19 +1,17 @@
-import EditorActionsManager from "./EditorActionsManager";
 import { EModalType } from "../ui/react-pathway-mapper";
+import EditorActionsManager from "./EditorActionsManager";
 
 export default class ContextMenuManager {
   private cy: any;
   private editor: EditorActionsManager;
-  private isCBioPortal: boolean;
   private handleOpen: (modalId: EModalType) => void;
   private undoRedoManager: any;
   private isCollaborative: any;
-  constructor(cy: any, editor: EditorActionsManager, isCBioPortal: boolean,
+  constructor(cy: any, editor: EditorActionsManager,
               handleOpen: (modalId: EModalType) => void, undoRedoManager: any,
               isCollaborative: boolean){
     this.cy = cy;
     this.editor = editor;
-    this.isCBioPortal = isCBioPortal;
     this.handleOpen = handleOpen;
     this.undoRedoManager = undoRedoManager;
     this.isCollaborative = isCollaborative;