diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index cf5fb43..0c5afe3 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -2,6 +2,10 @@ name: build on: [push, workflow_dispatch] +permissions: + contents: write + id-token: write + jobs: build: uses: datavisyn/github-workflows/.github/workflows/build-node.yml@main diff --git a/package.json b/package.json index 86be094..3bde0b4 100644 --- a/package.json +++ b/package.json @@ -2,7 +2,7 @@ "name": "coral_public", "description": "Coral is a web-based cohort analysis tool to interactively create, refine, and analyze patient cohorts.", "homepage": "https://caleydo.org", - "version": "3.2.0", + "version": "4.0.0", "author": { "name": "PatrickAdelberger", "email": "coral@caleydo.org", @@ -31,7 +31,7 @@ "dist": "mkdir lib && cd dist && tar cvzf ../lib/bundle.tar.gz *", "docs": "visyn_scripts docs", "lint:fix": "visyn_scripts lint --fix", - "lint": "visyn_scripts lint || true", + "lint": "visyn_scripts lint", "prepack": "yarn run build", "start": "visyn_scripts start --env workspace_mode=single", "storybook:build": "NODE_OPTIONS=--max_old_space_size=4096 build-storybook", @@ -52,17 +52,21 @@ "node": ">=16" }, "dependencies": { - "canvas-confetti": "^1.4.0", - "coral": "git+ssh://git@github.com/Caleydo/coral#semver:^4.1.0", - "ordino": "git+ssh://git@github.com/Caleydo/ordino#semver:^13.0.1", + "canvas-confetti": "^1.5.1", + "coral": "git+ssh://git@github.com:Caleydo/coral#semver:^5.0.0", + "ordino": "git+ssh://git@github.com:Caleydo/ordino#semver:^14.0.0", "react": "^16.13.0", "react-dom": "^16.13.0", "react-router-dom": "^5.2.0", - "visyn_scripts": "^1.1.1" + "visyn_scripts": "^4.1.0" + }, + "resolutions": { + "@types/react": "~18.2.0", + "@types/react-dom": "~18.2.0", + "react": "~18.2.0", + "react-dom": "~18.2.0" }, "devDependencies": { - "@types/react": "^16.14.6", - "@types/react-dom": "^16.9.5", "@types/react-router-dom": "^5.1.7", "mkdirp": "0.5.1", "tslint": "~5.20.1", diff --git a/src/LoginDialog.ts b/src/LoginDialog.ts index 1e003ec..e5a174c 100644 --- a/src/LoginDialog.ts +++ b/src/LoginDialog.ts @@ -6,10 +6,10 @@ export function create(_loginMenu: HTMLElement, loginDialog: HTMLElement) { if (localStorageValue !== null) { // check the checkbox if it was checked before - checkboxAcceptGenieTerms.checked = (localStorageValue === 'true'); + checkboxAcceptGenieTerms.checked = localStorageValue === 'true'; } - checkboxAcceptGenieTerms.addEventListener('change', function() { + checkboxAcceptGenieTerms.addEventListener('change', function listener() { localStorage.setItem(LOCALSTORAGE_ACCEPT_GENIE_TERMS, String(this.checked)); }); } diff --git a/src/assets/news/export_cohorts.png b/src/assets/news/v120_export_cohorts.png similarity index 100% rename from src/assets/news/export_cohorts.png rename to src/assets/news/v120_export_cohorts.png diff --git a/src/assets/news/new_session.png b/src/assets/news/v120_new_session.png similarity index 100% rename from src/assets/news/new_session.png rename to src/assets/news/v120_new_session.png diff --git a/src/assets/news/v200_plots-without-grid-lines.png b/src/assets/news/v200_plots-without-grid-lines.png new file mode 100644 index 0000000..b817de0 Binary files /dev/null and b/src/assets/news/v200_plots-without-grid-lines.png differ diff --git a/src/index.ts b/src/index.ts index 9bad3fb..e69de29 100644 --- a/src/index.ts +++ b/src/index.ts @@ -1,11 +0,0 @@ -// export * from './data'; -// export * from './Overview'; -// export * from './Taskview'; - -// export * from './app'; -// export * from './Cohort'; -// export * from './CohortInterfaces'; -// export * from './CohortRepresentations'; -// export * from './cohortview'; -// export * from './LoginDialog'; -// export * from './rest'; diff --git a/src/initialize.app.ts b/src/initialize.app.ts index 69d31f0..cbeea90 100644 --- a/src/initialize.app.ts +++ b/src/initialize.app.ts @@ -2,10 +2,10 @@ * Created by Caleydo Team on 31.08.2016. */ -import { App } from 'coral'; +import { Coral } from 'coral'; import loginDialog from './LoginDialog.html'; const APP_NAME = 'Coral'; document.title = APP_NAME; -const tdpApp = new App(APP_NAME, loginDialog); // assign to variable to avoid linting errors +const tdpApp = new Coral(APP_NAME, loginDialog); // assign to variable to avoid linting errors diff --git a/src/initialize.welcome.tsx b/src/initialize.welcome.tsx index e2865ab..aa6cdcd 100644 --- a/src/initialize.welcome.tsx +++ b/src/initialize.welcome.tsx @@ -1,12 +1,12 @@ import 'ordino/dist/robots.txt'; import * as React from 'react'; -import * as ReactDOM from 'react-dom'; -import { HashRouter, Route, Switch } from 'react-router-dom'; +import { createRoot } from 'react-dom/client'; +import { HashRouter, Switch, Route } from 'react-router-dom'; +import { RouterScrollToTop } from 'coral'; import { DatasetsPage, Error404Page, FeaturesPage, HelpPage, HomePage, NewsPage, PublicationPage } from './pages'; -import { RouterScrollToTop } from './utils/RouterScrollToTop'; -ReactDOM.render( +createRoot(document.querySelector('#welcome')).render( {/* A looks through its children s and @@ -45,5 +45,4 @@ ReactDOM.render( , - document.querySelector('#welcome'), ); diff --git a/src/menu/HelpTab.tsx b/src/menu/HelpTab.tsx index d5d6c00..5d5e479 100644 --- a/src/menu/HelpTab.tsx +++ b/src/menu/HelpTab.tsx @@ -1,16 +1,16 @@ -import {OrdinoFooter} from 'ordino'; +import { OrdinoFooter } from 'ordino'; import * as React from 'react'; -import {BrowserRouter} from 'react-router-dom'; -import {DevelopedByAffiliations} from '../pages/components/DevelopedByAffiliations'; -import {CoralHelpSection} from '../pages/components/CoralHelpSection'; +import { BrowserRouter } from 'react-router-dom'; +import { DevelopedByAffiliations } from '../pages/components/DevelopedByAffiliations'; +import { CoralHelpSection } from '../pages/components/CoralHelpSection'; export default function HelpTab() { - return <> - - - - - - - ; + return ( + + + + + + + ); } diff --git a/src/menu/index.ts b/src/menu/index.ts deleted file mode 100644 index 6a61e1a..0000000 --- a/src/menu/index.ts +++ /dev/null @@ -1 +0,0 @@ -export * from './HelpTab'; diff --git a/src/pages/DatasetsPage.tsx b/src/pages/DatasetsPage.tsx index 7426614..1538dd2 100644 --- a/src/pages/DatasetsPage.tsx +++ b/src/pages/DatasetsPage.tsx @@ -1,4 +1,4 @@ -import {HeaderNavigation, OrdinoFooter} from 'ordino'; +import { HeaderNavigation, OrdinoFooter } from 'ordino'; import * as React from 'react'; interface IDatasetPageCardProps { @@ -6,8 +6,7 @@ interface IDatasetPageCardProps { children?: React.ReactNode; } - -export function DatasetPageCard({title, children}: IDatasetPageCardProps) { +export function DatasetPageCard({ title, children }: IDatasetPageCardProps) { return (
@@ -18,30 +17,35 @@ export function DatasetPageCard({title, children}: IDatasetPageCardProps) { ); } - export function DatasetsPage() { return ( <> - +
-

Basic Datasets

+

+ Basic Datasets +

Sample annotation, gene expression, mutation, and copy number data

- cancergenome.nih.gov + + cancergenome.nih.gov +
@@ -50,13 +54,17 @@ export function DatasetsPage() {

Sample annotation, gene expression, mutation, and copy number data

- portals.broadinstitute.org/ccle + + portals.broadinstitute.org/ccle +
-

Depletion Sceen Data

+

+ Depletion Sceen Data +

@@ -64,21 +72,25 @@ export function DatasetsPage() {
- +
diff --git a/src/pages/Error404Page.tsx b/src/pages/Error404Page.tsx index 110a4d8..da54dca 100644 --- a/src/pages/Error404Page.tsx +++ b/src/pages/Error404Page.tsx @@ -1,16 +1,18 @@ import * as React from 'react'; -import {HeaderNavigation, OrdinoFooter} from 'ordino'; +import { HeaderNavigation, OrdinoFooter } from 'ordino'; export function Error404Page() { return ( <> - +
-

Page Not Found

+
+

Page Not Found

+
- + ); } diff --git a/src/pages/FeaturesPage.tsx b/src/pages/FeaturesPage.tsx index 1ec0ea8..dbb96e5 100644 --- a/src/pages/FeaturesPage.tsx +++ b/src/pages/FeaturesPage.tsx @@ -1,4 +1,4 @@ -import {HeaderNavigation, OrdinoFooter} from 'ordino'; +import { HeaderNavigation, OrdinoFooter } from 'ordino'; import * as React from 'react'; import areaChart from '../assets/feature_icons/areaChart.png'; import barChart from '../assets/feature_icons/barChart.png'; @@ -6,7 +6,7 @@ import boxPlot from '../assets/feature_icons/boxPlot.png'; import densityPlot from '../assets/feature_icons/densityPlot.png'; import scatterPlot from '../assets/feature_icons/scatterPlot.png'; import survivalPlot from '../assets/feature_icons/survivalPlot.png'; -import {FeatureCard} from './components/FeatureCard'; +import { FeatureCard } from './components/FeatureCard'; import intro from '../assets/welcome_tour/030_Workflow_Intro.svg'; import overview1 from '../assets/welcome_tour/100_Overview.svg'; import overview2 from '../assets/welcome_tour/110_Overview.svg'; @@ -22,71 +22,70 @@ import details from '../assets/welcome_tour/600_Details.svg'; export function FeaturesPage() { return ( <> - +
-