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dvmoritzschoeflthinkholtionchamparipuehringerdvvanessastoiber
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React 18 Migration (#58)
* Remove `|| true` to show eslint errors #693 * Run `lint:fix` to automatically fix formatting #693 * Add missing component `RouterScrollToTop` * Refactor src/app.ts into separate files src/app/* Caleydo/cohort#693 * Rename app/Cohort to app/Coral * Move colors to config/colors Caleydo/cohort#693 * Move rest to base/rest Caleydo/cohort#693 * Move ScrollLinker from util file to utils/ScrollLinker Caleydo/cohort#693 * Remove unused color schemes Caleydo/cohort#693 * Extract CohortColorSchema from util to separate file Caleydo/cohort#693 * Merge CohortColorSchema with config/colors Caleydo/cohort#693 * Move utilCustomEvents to base/events Caleydo/cohort#693 * Move utilIdTypes to config/entities Caleydo/cohort#693 * Move utilLabels to utils/labels Caleydo/cohort#693 * Merge Tooltip into AColumn and remove export Caleydo/cohort#693 * Rename event to event2 for nested event Caleydo/cohort#693 * Merge CohortInterfaces into app/interfaces Caleydo/cohort#693 * Use `ICohort` instead `Cohort` Caleydo/cohort#693 - Replace `Cohort` with `ICohort` were possible - Add interfaces `IInputCohort` and `IOutputCohort` - Move classes `InputCohort` and `OutputCohort` to Cohort.ts - Move public functions and properties from `Cohort` to interface `ICohort` - Move interfaces and enums from `Cohort` to app/interfacoes - Replace `Array<...>` with `...[]` syntax * Reorder functions in utlis/labels Caleydo/cohort#693 * Eslint and typescript errors (#56) * Upgrade python deps (#51) * Upgrade python deps * Switch back to #develop * Release 4.1.0 (#54) * prepare next dev version * Fix colors assignment in plots (#41) * Prepare github changes * Remove circleci * prepare next dev version * Use `Font Awesome 6 Free` in `font-family` (#39) * Use `Font Awesome 6 Free` in `font-family` Requires datavisyn/tdp_core#732 * Update Lineup to 4.6.2 Co-authored-by: Klaus Eckelt <[email protected]> * Update fontawesome * Merge visyn_scripts * prepare next dev version * Merged `d3_changes` into `develop` (#45) * use d3v7 and d3v3 imports remove depenencies to d3 add dependency to tdp_core * remove console log * Dev d3 merge fix (#47) * move RouterScrollToTop to coral_public * fix TS errors * move canvas-confetti to coral_public * update git dependencies Co-authored-by: Klaus Eckelt <[email protected]> * Automatically select root cohort if onboarding was already done (#48) * Autoselect rootcohort if onboarding was done #579 * format code * Remove grid lines from visualizations (#49) remove gridlines #400 * Upgrade python deps (#51) * Upgrade python deps * Switch back to #develop * prepare release 4.1.0 --------- Co-authored-by: Klaus Eckelt <[email protected]> Co-authored-by: anita-steiner <> Co-authored-by: Holger Stitz <[email protected]> Co-authored-by: Patrick <[email protected]> Co-authored-by: Michael Pühringer <[email protected]> * prepare next dev version * Migration to visyn_core (#55) * Migration to visyn_core * Linting * Upgrade deps --------- Co-authored-by: Michael Puehringer <[email protected]> * Fix cohort * Fix circular dependencies * Further cleanup * Fix async in loop * Import * Add todos for async inside loop errors --------- Co-authored-by: Michael Pühringer <[email protected]> Co-authored-by: Vanessa Stoiber <[email protected]> Co-authored-by: Klaus Eckelt <[email protected]> Co-authored-by: Holger Stitz <[email protected]> Co-authored-by: Patrick <[email protected]> Co-authored-by: dvvanessastoiber <[email protected]> Co-authored-by: Michael Puehringer <[email protected]> * bug: merge data subtype object * React 18 Migration * Fix typings * Fix client config typings * Pin ordino, tourdino * Add initial value to cohorts array * Cleanup * tsconfig * Update package.json --------- Co-authored-by: Holger Stitz <[email protected]> Co-authored-by: Champari Oltion <[email protected]> Co-authored-by: Michael Pühringer <[email protected]> Co-authored-by: Vanessa Stoiber <[email protected]> Co-authored-by: Klaus Eckelt <[email protected]> Co-authored-by: Patrick <[email protected]> Co-authored-by: dvvanessastoiber <[email protected]> Co-authored-by: Michael Puehringer <[email protected]> Co-authored-by: oltionchampari <[email protected]> Co-authored-by: Moritz Heckmann <[email protected]>
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‎package.json

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"devDependencies": {
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"@types/d3-selection": "^3.0.2",
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"@types/d3-transition": "^3.0.1",
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"@types/react": "^16.14.6",
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"@types/react-dom": "^16.9.5",
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"@types/react-router-dom": "^5.1.7",
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"mkdirp": "0.5.1",
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"tslint": "~5.20.1",
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"worker-loader": "^2.0.0"
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},
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"resolutions": {
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"@types/react": "~18.2.0",
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"@types/react-dom": "~18.2.0",
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"react": "~18.2.0",
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"react-dom": "~18.2.0"
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},
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"browser": {
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"fs": false,
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"os": false,

‎src/Cohort.ts

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/* eslint-disable @typescript-eslint/no-use-before-define */
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import { IDType, IDTypeLike, IDTypeManager, IRow, IServerColumn } from 'visyn_core';
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import { IDType, IDTypeLike, IDTypeManager } from 'visyn_core/idtype';
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import { IRow, IServerColumn } from 'visyn_core/base';
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import { IAllFilters, UniqueIdManager } from 'tdp_core';
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import {
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ECloneFilterTypes,

‎src/Tasks.ts

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import { IServerColumn } from 'visyn_core';
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import type { IServerColumn } from 'visyn_core/base';
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import { log } from './util';
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import { EElementProvType, IElement, IElementProvJSON, IElementProvJSONTask, ITask, ITaskRep, TaskType } from './app/interfaces';
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import { GeneScoreAttribute, PanelScoreAttribute, ServerColumnAttribute, SpecialAttribute } from './data/Attribute';

‎src/Taskview/SearchBar.ts

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import { select } from 'd3v7';
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import { IServerColumn } from 'visyn_core';
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import { IServerColumn } from 'visyn_core/base';
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import { IdTextPair, RestBaseUtils } from 'tdp_core';
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import { dataTypes, depletion, IDataSubtypeConfig, IDataTypeConfig } from 'tdp_publicdb';
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import { colors } from '../config/colors';

‎src/Taskview/Taskview.ts

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class TaskviewInput extends TaskviewTable {
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cohortOrder: number[];
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cohorts: IInputCohort[];
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cohorts: IInputCohort[] = [];
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usedColorsForCohorts = CoralColorSchema.COLOR_SCHEME.map((elem) => {
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return { color: elem, cohorts: [] };

‎src/app/Coral.ts

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import { select } from 'd3v7';
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import { ATDPApplication, CLUEGraphManager, IClientConfig, ITDPOptions, ProvenanceGraph } from 'tdp_core';
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import { ATDPApplication, CLUEGraphManager, ITDPOptions, ProvenanceGraph } from 'tdp_core';
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import { IClientConfig } from 'visyn_core/base';
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import { CoralApp, ICoralClientConfig } from './CoralApp';
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import { log } from '../util';
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‎src/app/CoralApp.ts

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import { select, Selection } from 'd3v7';
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import SplitGrid from 'split-grid';
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import { IServerColumn } from 'visyn_core';
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import {
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AppContext,
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CLUEGraphManager,
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IDatabaseViewDesc,
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IObjectRef,
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ITDPOptions,
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NotificationHandler,
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ObjectRefUtils,
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ProvenanceGraph,
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RestBaseUtils,
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} from 'tdp_core';
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import { IServerColumn, AppContext } from 'visyn_core/base';
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import { CLUEGraphManager, IDatabaseViewDesc, IObjectRef, ITDPOptions, NotificationHandler, ObjectRefUtils, ProvenanceGraph, RestBaseUtils } from 'tdp_core';
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import { cellline, tissue } from 'tdp_publicdb';
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import { Instance as TippyInstance } from 'tippy.js';
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import { createCohort, createCohortFromDB } from '../Cohort';

‎src/app/interfaces.ts

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import { IDType, IDTypeLike, IRow, IServerColumn } from 'visyn_core';
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import { IDType, IDTypeLike } from 'visyn_core/idtype';
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import { IServerColumn, IRow } from 'visyn_core/base';
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import { IAllFilters } from 'tdp_core';
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import type { IEntitySourceConfig } from '../config/entities';
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import {

‎src/base/rest.ts

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import { Ajax, AppContext, IRow } from 'visyn_core';
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import { Ajax, AppContext, IRow } from 'visyn_core/base';
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import { IParams } from 'tdp_core';
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import { deepCopy, log } from '../util';
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import {

‎src/common/config.ts

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*/
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import { Categories } from 'tdp_publicdb';
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import { IServerColumn } from 'visyn_core';
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import { IServerColumn } from 'visyn_core/base';
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import { ColumnDescUtils, IAdditionalColumnDesc } from 'tdp_core';
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/**

‎src/common/forms.ts

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*/
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import { SpeciesUtils, FormSubtype } from 'tdp_publicdb';
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import { IServerColumn } from 'visyn_core';
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import { IServerColumn } from 'visyn_core/base';
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import { FormElementType, IFormElement, IFormSelectOption, ValueCache, RestStorageUtils, LineupUtils, RestBaseUtils } from 'tdp_core';
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import { gene, IDataSourceConfig, tissue, cellline, dataSources, dataTypes, dataSubtypes, depletion, drugScreen } from './config';
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import { GeneUtils } from './GeneUtils';

‎src/data/Attribute.ts

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import { IAllFilters } from 'tdp_core';
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import { IDataTypeConfig, IDataSubtypeConfig, resolveDataTypes } from 'tdp_publicdb';
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import { IServerColumn } from 'visyn_core';
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import { IServerColumn } from 'visyn_core/base';
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import { IDataSubtypeConfig, IDataTypeConfig, resolveDataTypes } from 'tdp_publicdb';
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import { ICohort } from '../app/interfaces';
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import {
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HistRouteType,

‎src/data/IAttribute.ts

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import { IAllFilters, IServerColumn } from 'tdp_core';
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import { IAllFilters } from 'tdp_core';
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import { IServerColumn } from 'visyn_core/base';
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import { IDataSubtypeConfig } from 'tdp_publicdb';
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import { ICohort } from '../app/interfaces';
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import { INumRange, IEqualsList, HistRouteType } from '../base/interfaces';

‎src/phovea.ts

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* Copyright (c) The Caleydo Team. All rights reserved.
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* Licensed under the new BSD license, available at http://caleydo.org/license
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**************************************************************************** */
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import type { IRegistry } from 'visyn_core';
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import type { IRegistry } from 'visyn_core/plugin';
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export default function (registry: IRegistry) {
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// helper functions copied from tdp_core:
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/**
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* Set the base data-set
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*/
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actionFunction('chtSetDataset', 'setDatasetImpl', () => import('./Provenance/General.js'), {
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actionFunction('chtSetDataset', 'setDatasetImpl', () => import('./Provenance/General'), {
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// setDatasetImpl = function that acutally sets the dataset
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analytics: {
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category: 'data', // this one is a data operation (other options are visual, selections, layout, and analysis)
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/**
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* Add Cohorts
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*/
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actionFunction('addCohorts', 'addOverviewCohortImpl', () => import('./Provenance/CohortEV.js').then(), {
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actionFunction('addCohorts', 'addOverviewCohortImpl', () => import('./Provenance/CohortEV').then(), {
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//
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analytics: {
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/**
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* Remove Cohorts
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*/
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actionFunction('removeCohorts', 'removeOverviewCohortImpl', () => import('./Provenance/CohortEV.js').then(), {
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actionFunction('removeCohorts', 'removeOverviewCohortImpl', () => import('./Provenance/CohortEV').then(), {
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//
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analytics: {
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category: 'data', // this one is a data operation (other options are visual, selections, layout, and analysis)

‎src/phovea_registry.ts

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* Licensed under the new BSD license, available at http://caleydo.org/license
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**************************************************************************** */
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import { PluginRegistry } from 'visyn_core';
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import { PluginRegistry } from 'visyn_core/plugin';
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import reg from './phovea';
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/**

‎tsconfig.json

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"extends": "visyn_scripts/config/tsconfig.template.json",
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"compilerOptions": {
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"outDir": "./dist",
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"sourceMap": false,
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},
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"include": [
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"src/**/*.ts",

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