├── .nvmrc
├── data
    ├── __init__.py
    ├── parsers
    │   ├── __init__.py
    │   ├── israel.py
    │   └── okinawa.py
    ├── scripts
    │   ├── __init__.py
    │   ├── default_schema_values.py
    │   ├── validateAge.py
    │   ├── seasonal_R0_explainer.py
    │   ├── mapping.py
    │   ├── transform_ages.py
    │   └── transform_ages_v2.py
    ├── case-counts
    │   ├── owid
    │   │   ├── Turkmenistan.tsv
    │   │   └── Niue.tsv
    │   ├── india
    │   │   ├── IND-Goa***.tsv
    │   │   ├── IND-Punjab***.tsv
    │   │   ├── IND-Chandigarh***.tsv
    │   │   ├── IND-Uttarakhand***.tsv
    │   │   ├── IND-Bihar****.tsv
    │   │   ├── IND-Maharashtra***.tsv
    │   │   └── IND-Dadar Nagar Haveli.tsv
    │   ├── china
    │   │   ├── CHN-Xizang.tsv
    │   │   ├── CHN-Qinghai.tsv
    │   │   └── CHN-Ningxia.tsv
    │   └── ecdc
    │   │   └── Saint Barthelemy.tsv
    ├── Pipfile
    ├── paths.py
    ├── hospital-data
    │   ├── hospital_eurostat.tsv
    │   └── ICU_asia.tsv
    └── Makefile
├── .github
    ├── pull_request_template.md
    ├── ISSUE_TEMPLATE
    │   ├── bug_report.md
    │   ├── feature_request.md
    │   └── config.yml
    └── workflows
    │   └── eslint.yml
├── 3rdparty
    └── __empty-module
    │   ├── index.js
    │   └── package.json
├── config
    ├── jest
    │   ├── setupDotenv.js
    │   ├── mocks
    │   │   ├── fileMock.js
    │   │   ├── mockReactChildrenUtilities.js
    │   │   ├── mockUseDebounce.js
    │   │   ├── mockReactI18next.js
    │   │   └── mockPopperJS.js
    │   ├── jest.eslint.config.js
    │   └── jest.config.js
    ├── dotenv
    │   └── index.js
    ├── next
    │   ├── lib
    │   │   ├── CustomWebpackConfig.ts
    │   │   ├── addWebpackLoader.ts
    │   │   ├── addWebpackConfig.ts
    │   │   └── addWebpackPlugin.ts
    │   ├── withWorker.ts
    │   ├── withEnvironment.ts
    │   ├── withRaw.ts
    │   ├── withoutMinification.ts
    │   ├── withExtraWatch.ts
    │   ├── withMdx.ts
    │   ├── withIgnore.ts
    │   ├── withPolyfills.ts
    │   ├── withLodash.ts
    │   ├── withSvg.ts
    │   └── withImages.ts
    └── nodemon
    │   ├── serve.json
    │   ├── stylelint.json
    │   ├── stylelint.fix.json
    │   ├── lint.json
    │   ├── lint.fix.json
    │   ├── dev.json
    │   ├── eslint.json
    │   ├── eslint.fix.json
    │   ├── analyze.json
    │   └── prod.json
├── public
    ├── robots.txt
    ├── favicon.ico
    ├── social-1200x600.png
    ├── icons
    │   ├── favicon-16x16.png
    │   ├── favicon-32x32.png
    │   ├── favicon-96x96.png
    │   ├── mstile-70x70.png
    │   ├── apple-touch-icon.png
    │   ├── favicon-128x128.png
    │   ├── favicon-196x196.png
    │   ├── mstile-144x144.png
    │   ├── mstile-150x150.png
    │   ├── mstile-310x150.png
    │   ├── mstile-310x310.png
    │   ├── social-1200x600.png
    │   ├── android-chrome-36x36.png
    │   ├── android-chrome-48x48.png
    │   ├── android-chrome-72x72.png
    │   ├── android-chrome-96x96.png
    │   ├── android-chrome-144x144.png
    │   ├── android-chrome-192x192.png
    │   ├── android-chrome-256x256.png
    │   ├── android-chrome-384x384.png
    │   ├── android-chrome-512x512.png
    │   ├── apple-touch-icon-57x57.png
    │   ├── apple-touch-icon-60x60.png
    │   ├── apple-touch-icon-72x72.png
    │   ├── apple-touch-icon-76x76.png
    │   ├── apple-touch-icon-114x114.png
    │   ├── apple-touch-icon-120x120.png
    │   ├── apple-touch-icon-144x144.png
    │   ├── apple-touch-icon-152x152.png
    │   ├── apple-touch-icon-180x180.png
    │   ├── apple-touch-icon-precomposed.png
    │   ├── apple-touch-icon-114x114-precomposed.png
    │   ├── apple-touch-icon-120x120-precomposed.png
    │   ├── apple-touch-icon-144x144-precomposed.png
    │   ├── apple-touch-icon-152x152-precomposed.png
    │   ├── apple-touch-icon-180x180-precomposed.png
    │   ├── apple-touch-icon-57x57-precomposed.png
    │   ├── apple-touch-icon-60x60-precomposed.png
    │   ├── apple-touch-icon-72x72-precomposed.png
    │   └── apple-touch-icon-76x76-precomposed.png
    └── manifest.json
├── src
    ├── types
    │   ├── jpg-module.d.ts
    │   ├── png-module.d.ts
    │   ├── @next
    │   │   └── mdx.d.ts
    │   ├── next-compose-plugins.d.ts
    │   ├── next-runtime-dotenv.d.ts
    │   ├── json-module.d.ts
    │   ├── md-module.d.ts
    │   ├── mdx-module.d.ts
    │   ├── jsurl.d.ts
    │   ├── @nuxt
    │   │   └── friendly-errors-webpack-plugin.d.ts
    │   ├── next-transpile-modules.d.ts
    │   ├── styled.d.ts
    │   ├── glob-all.d.ts
    │   ├── create-color.d.ts
    │   ├── Intl.d.ts
    │   ├── svg-module.d.ts
    │   ├── allow-methods.d.ts
    │   ├── ajv-i18n.d.ts
    │   ├── assets.d.ts
    │   ├── size-plugin.d.ts
    │   ├── threads-plugin.d.ts
    │   ├── stylelint-bare-webpack-plugin.d.ts
    │   ├── remark-rehype.d.ts
    │   ├── react-awesome-popover.d.ts
    │   ├── hot-module.d.ts
    │   ├── redux-immutable-state-invariant.d.ts
    │   ├── core-js.d.ts
    │   ├── preload-webpack-plugin.d.ts
    │   ├── jest.d.ts
    │   ├── formik.d.ts
    │   └── recharts.d.ts
    ├── pages
    │   ├── faq.tsx
    │   ├── index.tsx
    │   ├── print.tsx
    │   ├── team.tsx
    │   ├── _error.tsx
    │   ├── 404.tsx
    │   ├── updates.tsx
    │   └── about.tsx
    ├── styles
    │   ├── components
    │   │   ├── SpinBox.scss
    │   │   ├── Disclaimer.scss
    │   │   ├── Layout.scss
    │   │   ├── Team.scss
    │   │   ├── NotFound.scss
    │   │   ├── DeterministicLinePlot.scss
    │   │   ├── Footer.scss
    │   │   ├── Popover.scss
    │   │   ├── Loading.scss
    │   │   ├── LanguageSwitcher.scss
    │   │   ├── ErrorPage.scss
    │   │   ├── ModalButtonExport.scss
    │   │   ├── SimulationControls.scss
    │   │   ├── ModalButtonSharing.scss
    │   │   ├── NavigationBar.scss
    │   │   ├── FormHelpButton.scss
    │   │   ├── CaseCountsUploader.scss
    │   │   ├── ResponsiveTooltipContent.scss
    │   │   ├── ScenarioTitle.scss
    │   │   ├── OutcomesDetailsTable.scss
    │   │   └── SeverityTable.scss
    │   ├── react-loader-spinner.scss
    │   ├── katex.scss
    │   ├── animate.scss
    │   ├── _mixins.scss
    │   └── font-family-system.scss
    ├── helpers
    │   ├── appendDash.ts
    │   ├── ErrorArray.ts
    │   ├── uuid.ts
    │   ├── copyToClipboard.ts
    │   ├── getOrThrow.ts
    │   ├── getCopyrightYearRange.ts
    │   ├── useTranslationSafe.ts
    │   ├── numberFormat.ts
    │   ├── errorPrototypeTojson.ts
    │   ├── saveTextFile.ts
    │   ├── readFile.ts
    │   ├── getVersionString.ts
    │   ├── getFormikErrors.ts
    │   └── types.ts
    ├── components
    │   ├── Main
    │   │   ├── ScenarioLoader
    │   │   │   ├── ScenarioOption.ts
    │   │   │   ├── ScenarioLoaderUploadInstructionsText.mdx
    │   │   │   ├── ScenarioLoaderListItem.tsx
    │   │   │   ├── ScenarioLoaderCard.tsx
    │   │   │   └── __tests__
    │   │   │   │   └── ScenarioLoader.test.tsx
    │   │   ├── Controls
    │   │   │   ├── filenames.ts
    │   │   │   ├── UrlTextInput.tsx
    │   │   │   └── PlotControls.tsx
    │   │   ├── PrintPreview
    │   │   │   ├── PrintDisclaimer.mdx
    │   │   │   └── dateFormat.ts
    │   │   ├── Results
    │   │   │   ├── chartHelper.ts
    │   │   │   └── PlotSpinner.tsx
    │   │   ├── Scenario
    │   │   │   ├── SeverityCardInfo.mdx
    │   │   │   └── ScenarioCardContainment.tsx
    │   │   └── CaseCounts
    │   │   │   └── CaseCountsUploaderInstructionsText.mdx
    │   ├── Print
    │   │   └── PrintPage.tsx
    │   ├── Wrappers
    │   │   └── Popover.tsx
    │   ├── Form
    │   │   ├── FormDropdownOption.ts
    │   │   ├── FormLabel.tsx
    │   │   ├── HelpLabel.tsx
    │   │   ├── __tests__
    │   │   │   ├── HelpLabel.test.tsx
    │   │   │   └── FormLabel.test.tsx
    │   │   ├── SpinBox.tsx
    │   │   ├── FormCustom.tsx
    │   │   ├── RangeSpinBox.tsx
    │   │   ├── FormHelpButton.tsx
    │   │   ├── FormSwitch.tsx
    │   │   └── FormRangeSpinBox.tsx
    │   ├── Link
    │   │   ├── LinkExternal.tsx
    │   │   └── Link.tsx
    │   ├── Layout
    │   │   ├── ColCustom.tsx
    │   │   ├── MdxWrapper.tsx
    │   │   ├── NavigationLink.tsx
    │   │   └── Layout.tsx
    │   ├── Updates
    │   │   └── UpdatesPage.tsx
    │   ├── NotFound
    │   │   └── NotFoundPage.tsx
    │   ├── Buttons
    │   │   ├── LinkButton.tsx
    │   │   └── ClipboardButton.tsx
    │   ├── Faq
    │   │   ├── Faq.tsx
    │   │   └── FaqTableOfContents.tsx
    │   ├── Loading
    │   │   └── Loading.tsx
    │   ├── Common
    │   │   ├── ButtonTransparent.tsx
    │   │   └── Plausible.tsx
    │   └── Team
    │   │   └── TeamPage.tsx
    ├── assets
    │   └── img
    │   │   ├── youtube-tutorial-thumbnail.jpg
    │   │   └── github.svg
    ├── algorithms
    │   ├── types
    │   │   ├── TimeSeries.types.ts
    │   │   └── convert.ts
    │   └── utils
    │   │   ├── exceptions.ts
    │   │   ├── sample.ts
    │   │   └── suggestNextMitigationInterval.ts
    ├── state
    │   ├── app
    │   │   └── init.actions.ts
    │   ├── router
    │   │   └── router.selectors.ts
    │   ├── ui
    │   │   ├── ui.actions.ts
    │   │   └── ui.sagas.ts
    │   ├── algorithm
    │   │   ├── algorithm.state.ts
    │   │   ├── algorithm.selectors.ts
    │   │   ├── algorithm.actions.ts
    │   │   ├── algorithm.sagas.ts
    │   │   └── algorithm.reducer.ts
    │   ├── error
    │   │   ├── error.actions.ts
    │   │   └── error.reducer.ts
    │   ├── settings
    │   │   ├── settings.sagas.ts
    │   │   ├── settings.state.ts
    │   │   ├── settings.actions.ts
    │   │   └── settings.selectors.ts
    │   ├── util
    │   │   └── fsaImmerReducer.ts
    │   └── sagas.ts
    ├── workers
    │   └── algorithm
    │   │   ├── worker.types.ts
    │   │   ├── worker.ts
    │   │   └── index.ts
    ├── io
    │   ├── encoding
    │   │   ├── v1
    │   │   │   └── encode.ts
    │   │   ├── encode.ts
    │   │   ├── errors.ts
    │   │   ├── decode.ts
    │   │   └── versioning.ts
    │   ├── serialization
    │   │   ├── fromUrl.ts
    │   │   ├── toUrl.ts
    │   │   ├── versioning.ts
    │   │   ├── deserialize.ts
    │   │   └── serialize.ts
    │   ├── parsingCsv
    │   │   └── errors.ts
    │   └── defaults
    │   │   ├── __tests__
    │   │       └── getCaseCountsData.test.ts
    │   │   ├── getScenarioData.ts
    │   │   └── getAgeDistributionData.ts
    ├── initialize.ts
    ├── constants.ts
    └── i18n
    │   └── detectLocale.ts
├── vercel.png
├── .nowignore
├── next-env.d.ts
├── next.config.js
├── cypress.json
├── lib
    ├── EnvVarError.d.ts
    ├── getenv.d.ts
    ├── getBuildUrl.ts
    ├── getBuildNumber.ts
    ├── clear.js
    ├── findModuleRoot.d.ts
    ├── findModuleRoot.js
    ├── getenv.js
    ├── EnvVarError.js
    ├── getGitBranch.ts
    └── getGitCommitHash.ts
├── schemas
    ├── _SchemaVer.yml
    ├── ColorHex.yml
    ├── Percentage.yml
    ├── AgeGroup.yml
    ├── Integer.yml
    ├── ScenarioArray.yml
    ├── CaseCountsArray.yml
    ├── AgeDistributionArray.yml
    ├── IntegerPositive.yml
    ├── IntegerNonNegative.yml
    ├── ScenarioData.yml
    ├── SeverityDistributionArray.yml
    ├── AgeDistributionDatum.yml
    ├── ScenarioDatumMitigation.yml
    ├── CaseCountsData.yml
    ├── PercentageRange.yml
    ├── AgeDistributionData.yml
    ├── NumericRangeNonNegative.yml
    ├── SeverityDistributionData.yml
    ├── ScenarioDatumSimulation.yml
    ├── MitigationInterval.yml
    ├── DateRange.yml
    ├── Shareable.yml
    ├── ScenarioDatum.yml
    ├── SeverityDistributionDatum.yml
    ├── CaseCountsDatum.yml
    ├── ScenarioDatumPopulation.yml
    └── ScenarioDatumEpidemiological.yml
├── codecov.yml
├── update_data.sh
├── .browserslistrc
├── .prettierrc
├── .gitignore
├── .editorconfig
├── .eslintignore
├── .prettierignore
├── postcss.config.js
├── docker
    ├── node-git-alpine
    │   └── Dockerfile
    ├── docker-compose.codeclimate.yml
    ├── python-pip
    │   └── Dockerfile
    ├── docker-compose.dev.yml
    └── docker-compose.data.yml
├── .yarnrc
├── tools
    ├── install-awscli.sh
    └── trigger-data-update.sh
├── .env.vercel
├── data_update.sh
├── now.json
├── LICENSE
├── .snyk
├── CONTRIBUTING.md
├── .travis.yml
└── stylelint.config.js


/.nvmrc:
--------------------------------------------------------------------------------
1 | 14.4.0
2 | 


--------------------------------------------------------------------------------
/data/__init__.py:
--------------------------------------------------------------------------------
1 | 


--------------------------------------------------------------------------------
/data/parsers/__init__.py:
--------------------------------------------------------------------------------
1 | 


--------------------------------------------------------------------------------
/data/scripts/__init__.py:
--------------------------------------------------------------------------------
1 | 


--------------------------------------------------------------------------------
/.github/pull_request_template.md:
--------------------------------------------------------------------------------
1 | 


--------------------------------------------------------------------------------
/3rdparty/__empty-module/index.js:
--------------------------------------------------------------------------------
1 | 


--------------------------------------------------------------------------------
/config/jest/setupDotenv.js:
--------------------------------------------------------------------------------
1 | require('../dotenv')
2 | 


--------------------------------------------------------------------------------
/public/robots.txt:
--------------------------------------------------------------------------------
1 | User-agent: *
2 | Disallow:
3 | 


--------------------------------------------------------------------------------
/src/types/jpg-module.d.ts:
--------------------------------------------------------------------------------
1 | declare module '*.jpg'
2 | 


--------------------------------------------------------------------------------
/src/types/png-module.d.ts:
--------------------------------------------------------------------------------
1 | declare module '*.png'
2 | 


--------------------------------------------------------------------------------
/src/types/@next/mdx.d.ts:
--------------------------------------------------------------------------------
1 | declare module '@next/mdx'
2 | 


--------------------------------------------------------------------------------
/config/jest/mocks/fileMock.js:
--------------------------------------------------------------------------------
1 | module.exports = __filename
2 | 


--------------------------------------------------------------------------------
/src/pages/faq.tsx:
--------------------------------------------------------------------------------
1 | export { Faq as default } from 'src/components/Faq/Faq'
2 | 


--------------------------------------------------------------------------------
/src/styles/components/SpinBox.scss:
--------------------------------------------------------------------------------
1 | .spinbox {
2 |   padding: 20px;
3 | }
4 | 


--------------------------------------------------------------------------------
/src/types/next-compose-plugins.d.ts:
--------------------------------------------------------------------------------
1 | declare module 'next-compose-plugins'
2 | 


--------------------------------------------------------------------------------
/src/types/next-runtime-dotenv.d.ts:
--------------------------------------------------------------------------------
1 | declare module 'next-runtime-dotenv'
2 | 


--------------------------------------------------------------------------------
/src/pages/index.tsx:
--------------------------------------------------------------------------------
1 | export { Main as default } from 'src/components/Main/Main'
2 | 


--------------------------------------------------------------------------------
/vercel.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/vercel.png


--------------------------------------------------------------------------------
/src/pages/print.tsx:
--------------------------------------------------------------------------------
1 | export { PrintPage as default } from 'src/components/Print/PrintPage'
2 | 


--------------------------------------------------------------------------------
/src/pages/team.tsx:
--------------------------------------------------------------------------------
1 | export { TeamPage as default } from 'src/components/Team/TeamPage'
2 | 


--------------------------------------------------------------------------------
/.nowignore:
--------------------------------------------------------------------------------
1 | .build
2 | .cache
3 | .github
4 | .ignore
5 | .reports
6 | src/.generated/latest
7 | 


--------------------------------------------------------------------------------
/next-env.d.ts:
--------------------------------------------------------------------------------
1 | /// <reference types="next" />
2 | /// <reference types="next/types/global" />
3 | 


--------------------------------------------------------------------------------
/next.config.js:
--------------------------------------------------------------------------------
1 | import config from './config/next/next.config'
2 | 
3 | module.exports = config
4 | 


--------------------------------------------------------------------------------
/public/favicon.ico:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/favicon.ico


--------------------------------------------------------------------------------
/src/pages/_error.tsx:
--------------------------------------------------------------------------------
1 | export { ErrorPage as default } from 'src/components/Error/ErrorPage'
2 | 


--------------------------------------------------------------------------------
/src/helpers/appendDash.ts:
--------------------------------------------------------------------------------
1 | export function appendDash(str: string) {
2 |   return ` - ${str}`
3 | }
4 | 


--------------------------------------------------------------------------------
/src/pages/404.tsx:
--------------------------------------------------------------------------------
1 | export { NotFoundPage as default } from 'src/components/NotFound/NotFoundPage'
2 | 


--------------------------------------------------------------------------------
/src/pages/updates.tsx:
--------------------------------------------------------------------------------
1 | export { UpdatesPage as default } from 'src/components/Updates/UpdatesPage'
2 | 


--------------------------------------------------------------------------------
/config/jest/mocks/mockReactChildrenUtilities.js:
--------------------------------------------------------------------------------
1 | module.exports = {
2 |   onlyText: (text) => text,
3 | }
4 | 


--------------------------------------------------------------------------------
/config/jest/mocks/mockUseDebounce.js:
--------------------------------------------------------------------------------
1 | export function useDebouncedCallback(f) {
2 |   return [f]
3 | }
4 | 


--------------------------------------------------------------------------------
/src/pages/about.tsx:
--------------------------------------------------------------------------------
1 | import About from 'src/components/About/About.mdx'
2 | 
3 | export default About
4 | 


--------------------------------------------------------------------------------
/public/social-1200x600.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/social-1200x600.png


--------------------------------------------------------------------------------
/src/helpers/ErrorArray.ts:
--------------------------------------------------------------------------------
1 | export class ErrorArray extends Error {
2 |   public readonly errors?: string[]
3 | }
4 | 


--------------------------------------------------------------------------------
/public/icons/favicon-16x16.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/favicon-16x16.png


--------------------------------------------------------------------------------
/public/icons/favicon-32x32.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/favicon-32x32.png


--------------------------------------------------------------------------------
/public/icons/favicon-96x96.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/favicon-96x96.png


--------------------------------------------------------------------------------
/public/icons/mstile-70x70.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/mstile-70x70.png


--------------------------------------------------------------------------------
/src/styles/components/Disclaimer.scss:
--------------------------------------------------------------------------------
1 | @import '../variables';
2 | 
3 | .modal-title {
4 |   text-align: center;
5 | }
6 | 


--------------------------------------------------------------------------------
/src/types/json-module.d.ts:
--------------------------------------------------------------------------------
1 | declare module '*.json' {
2 |   const content: object
3 |   export default content
4 | }
5 | 


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon.png


--------------------------------------------------------------------------------
/public/icons/favicon-128x128.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/favicon-128x128.png


--------------------------------------------------------------------------------
/public/icons/favicon-196x196.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/favicon-196x196.png


--------------------------------------------------------------------------------
/public/icons/mstile-144x144.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/mstile-144x144.png


--------------------------------------------------------------------------------
/public/icons/mstile-150x150.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/mstile-150x150.png


--------------------------------------------------------------------------------
/public/icons/mstile-310x150.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/mstile-310x150.png


--------------------------------------------------------------------------------
/public/icons/mstile-310x310.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/mstile-310x310.png


--------------------------------------------------------------------------------
/public/icons/social-1200x600.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/social-1200x600.png


--------------------------------------------------------------------------------
/cypress.json:
--------------------------------------------------------------------------------
1 | {
2 |   "baseUrl": "http://localhost:3000",
3 |   "env": {
4 |     "BASE_URL": "http://localhost:3000"
5 |   }
6 | }
7 | 


--------------------------------------------------------------------------------
/src/styles/components/Layout.scss:
--------------------------------------------------------------------------------
1 | // Some margin for non scenario views
2 | main > .container {
3 |   padding-top: 20px;
4 | }
5 | 


--------------------------------------------------------------------------------
/src/styles/react-loader-spinner.scss:
--------------------------------------------------------------------------------
1 | @import '../../node_modules/react-loader-spinner/dist/loader/css/react-spinner-loader.css';
2 | 


--------------------------------------------------------------------------------
/public/icons/android-chrome-36x36.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/android-chrome-36x36.png


--------------------------------------------------------------------------------
/public/icons/android-chrome-48x48.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/android-chrome-48x48.png


--------------------------------------------------------------------------------
/public/icons/android-chrome-72x72.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/android-chrome-72x72.png


--------------------------------------------------------------------------------
/public/icons/android-chrome-96x96.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/android-chrome-96x96.png


--------------------------------------------------------------------------------
/src/components/Main/ScenarioLoader/ScenarioOption.ts:
--------------------------------------------------------------------------------
1 | export interface ScenarioOption {
2 |   label: string
3 |   value: string
4 | }
5 | 


--------------------------------------------------------------------------------
/src/types/md-module.d.ts:
--------------------------------------------------------------------------------
1 | declare module '*.md' {
2 |   const MDXComponent: () => JSX.Element
3 |   export default MDXComponent
4 | }
5 | 


--------------------------------------------------------------------------------
/src/types/mdx-module.d.ts:
--------------------------------------------------------------------------------
1 | declare module '*.mdx' {
2 |   const MDXComponent: () => JSX.Element
3 |   export default MDXComponent
4 | }
5 | 


--------------------------------------------------------------------------------
/public/icons/android-chrome-144x144.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/android-chrome-144x144.png


--------------------------------------------------------------------------------
/public/icons/android-chrome-192x192.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/android-chrome-192x192.png


--------------------------------------------------------------------------------
/public/icons/android-chrome-256x256.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/android-chrome-256x256.png


--------------------------------------------------------------------------------
/public/icons/android-chrome-384x384.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/android-chrome-384x384.png


--------------------------------------------------------------------------------
/public/icons/android-chrome-512x512.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/android-chrome-512x512.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-57x57.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-57x57.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-60x60.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-60x60.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-72x72.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-72x72.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-76x76.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-76x76.png


--------------------------------------------------------------------------------
/src/styles/katex.scss:
--------------------------------------------------------------------------------
1 | /* stylelint-disable */
2 | 
3 | @import '../../node_modules/katex/dist/katex.css';
4 | 
5 | /* stylelint-enable */
6 | 


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-114x114.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-114x114.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-120x120.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-120x120.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-144x144.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-144x144.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-152x152.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-152x152.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-180x180.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-180x180.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-precomposed.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-precomposed.png


--------------------------------------------------------------------------------
/src/assets/img/youtube-tutorial-thumbnail.jpg:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/src/assets/img/youtube-tutorial-thumbnail.jpg


--------------------------------------------------------------------------------
/src/types/jsurl.d.ts:
--------------------------------------------------------------------------------
1 | declare module 'jsurl' {
2 |   function stringify(o: Record<string, any>): string
3 |   function parse(s: string): any
4 | }
5 | 


--------------------------------------------------------------------------------
/lib/EnvVarError.d.ts:
--------------------------------------------------------------------------------
1 | export declare class EnvVarError extends TypeError {
2 |   public constructor(key: string, value: string | null | undefined)
3 | }
4 | 


--------------------------------------------------------------------------------
/schemas/_SchemaVer.yml:
--------------------------------------------------------------------------------
1 | $schema: http://json-schema.org/draft-07/schema
2 | $id: _SchemaVer
3 | title: _SchemaVer
4 | 
5 | type: string
6 | const: 2.2.0
7 | 


--------------------------------------------------------------------------------
/src/algorithms/types/TimeSeries.types.ts:
--------------------------------------------------------------------------------
1 | export interface TimePoint {
2 |   t: number
3 |   y: number
4 | }
5 | 
6 | export type TimeSeries = TimePoint[]
7 | 


--------------------------------------------------------------------------------
/.github/ISSUE_TEMPLATE/bug_report.md:
--------------------------------------------------------------------------------
1 | ---
2 | name: 🐛 Bug Report
3 | about: Tell us if something is broken
4 | labels: t:bug, help wanted, needs triage
5 | ---
6 | 


--------------------------------------------------------------------------------
/codecov.yml:
--------------------------------------------------------------------------------
1 | coverage:
2 |   parsers:
3 |     javascript:
4 |       enable_partials: yes
5 | 
6 | comment:
7 |   layout: 'diff, files'
8 |   require_changes: true
9 | 


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-114x114-precomposed.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-114x114-precomposed.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-120x120-precomposed.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-120x120-precomposed.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-144x144-precomposed.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-144x144-precomposed.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-152x152-precomposed.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-152x152-precomposed.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-180x180-precomposed.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-180x180-precomposed.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-57x57-precomposed.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-57x57-precomposed.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-60x60-precomposed.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-60x60-precomposed.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-72x72-precomposed.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-72x72-precomposed.png


--------------------------------------------------------------------------------
/public/icons/apple-touch-icon-76x76-precomposed.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/neherlab/covid19_scenarios/HEAD/public/icons/apple-touch-icon-76x76-precomposed.png


--------------------------------------------------------------------------------
/schemas/ColorHex.yml:
--------------------------------------------------------------------------------
1 | $schema: http://json-schema.org/draft-07/schema
2 | $id: ColorHex
3 | title: ColorHex
4 | 
5 | type: string
6 | pattern: ^#(?:[0-9a-fA-F]{3}){1,2}$
7 | 


--------------------------------------------------------------------------------
/schemas/Percentage.yml:
--------------------------------------------------------------------------------
1 | $schema: http://json-schema.org/draft-07/schema
2 | $id: Percentage
3 | title: Percentage
4 | 
5 | type: number
6 | minimum: 0
7 | maximum: 100
8 | 


--------------------------------------------------------------------------------
/src/styles/components/Team.scss:
--------------------------------------------------------------------------------
1 | .team-table {
2 |   width: 100%;
3 |   margin: 15px;
4 |   margin-bottom: 20px;
5 |   img {
6 |     border-radius: 50%;
7 |   }
8 | }
9 | 


--------------------------------------------------------------------------------
/update_data.sh:
--------------------------------------------------------------------------------
1 | python3 covid19_scenarios_data/parse_all.py --fetch --output-case src/assets/data/case_counts.json --output-population src/assets/data/population.json
2 | 


--------------------------------------------------------------------------------
/.browserslistrc:
--------------------------------------------------------------------------------
 1 | [production]
 2 | defaults
 3 | cover 99.5%
 4 | since 2013
 5 | ie >= 10
 6 | 
 7 | [development]
 8 | last 5 Chrome versions
 9 | last 5 Firefox versions
10 | 


--------------------------------------------------------------------------------
/lib/getenv.d.ts:
--------------------------------------------------------------------------------
1 | export function getenv(key: string, defaultValue?: string | null): string
2 | 
3 | export function getbool(key: string, defaultValue?: boolean | null): boolean
4 | 


--------------------------------------------------------------------------------
/src/state/app/init.actions.ts:
--------------------------------------------------------------------------------
1 | import actionCreatorFactory from 'typescript-fsa'
2 | 
3 | const action = actionCreatorFactory('App')
4 | 
5 | export const init = action('init')
6 | 


--------------------------------------------------------------------------------
/.github/ISSUE_TEMPLATE/feature_request.md:
--------------------------------------------------------------------------------
1 | ---
2 | name: 🙋 Feature Request
3 | about: You have an idea? Suggest an improvement!
4 | labels: t:feat, help wanted, needs triage
5 | ---
6 | 


--------------------------------------------------------------------------------
/src/types/@nuxt/friendly-errors-webpack-plugin.d.ts:
--------------------------------------------------------------------------------
1 | import FriendlyErrorsWebpackPlugin from '@types/friendly-errors-webpack-plugin'
2 | 
3 | export default FriendlyErrorsWebpackPlugin
4 | 


--------------------------------------------------------------------------------
/src/types/next-transpile-modules.d.ts:
--------------------------------------------------------------------------------
1 | declare module 'next-transpile-modules' {
2 |   export default function getWithTranspileModules(transpiledModules?: (RegExp | string)[])
3 | }
4 | 


--------------------------------------------------------------------------------
/lib/getBuildUrl.ts:
--------------------------------------------------------------------------------
1 | import { getenv } from './getenv'
2 | 
3 | export function getBuildUrl() {
4 |   return getenv('TRAVIS_BUILD_WEB_URL', null) ?? getenv('CIRCLE_BUILD_URL', null)
5 | }
6 | 


--------------------------------------------------------------------------------
/src/styles/components/NotFound.scss:
--------------------------------------------------------------------------------
 1 | .h1-notfound {
 2 |   padding: 2rem;
 3 |   color: #fff;
 4 |   background-color: #a72a33;
 5 | }
 6 | 
 7 | .h3-notfound {
 8 |   margin-top: 50px;
 9 | }
10 | 


--------------------------------------------------------------------------------
/src/workers/algorithm/worker.types.ts:
--------------------------------------------------------------------------------
1 | import { AlgorithmResult } from '../../algorithms/types/Result.types'
2 | 
3 | export interface MessageData {
4 |   result: AlgorithmResult
5 |   error: string
6 | }
7 | 


--------------------------------------------------------------------------------
/src/components/Print/PrintPage.tsx:
--------------------------------------------------------------------------------
1 | import React from 'react'
2 | 
3 | import { PrintPreview } from '../Main/PrintPreview/PrintPreview'
4 | 
5 | export function PrintPage() {
6 |   return <PrintPreview />
7 | }
8 | 


--------------------------------------------------------------------------------
/src/styles/components/DeterministicLinePlot.scss:
--------------------------------------------------------------------------------
 1 | .legend {
 2 |   cursor: pointer;
 3 | }
 4 | 
 5 | .legend-inactive {
 6 |   color: #a9a9a9;
 7 |   text-decoration: line-through;
 8 |   cursor: pointer;
 9 | }
10 | 


--------------------------------------------------------------------------------
/lib/getBuildNumber.ts:
--------------------------------------------------------------------------------
1 | import { getenv } from './getenv'
2 | 
3 | export function getBuildNumber() {
4 |   return getenv('TRAVIS_BUILD_NUMBER', null) ?? getenv('BUILD_ID', null) ?? getenv('CIRCLE_BUILD_NUM', null)
5 | }
6 | 


--------------------------------------------------------------------------------
/src/helpers/uuid.ts:
--------------------------------------------------------------------------------
 1 | import { v4 } from 'uuid'
 2 | 
 3 | import type { Id } from './types'
 4 | 
 5 | export type UUIDv4 = Id<'UUIDv4'>
 6 | 
 7 | export function uuidv4(): UUIDv4 {
 8 |   return v4() as UUIDv4
 9 | }
10 | 


--------------------------------------------------------------------------------
/.prettierrc:
--------------------------------------------------------------------------------
 1 | {
 2 |   "arrowParens": "always",
 3 |   "printWidth": 120,
 4 |   "proseWrap": "always",
 5 |   "quoteProps": "consistent",
 6 |   "semi": false,
 7 |   "singleQuote": true,
 8 |   "trailingComma": "all"
 9 | }
10 | 


--------------------------------------------------------------------------------
/src/types/styled.d.ts:
--------------------------------------------------------------------------------
1 | /* eslint-disable @typescript-eslint/no-empty-interface */
2 | import { Theme } from 'src/theme'
3 | 
4 | declare module 'styled-components' {
5 |   export declare interface DefaultTheme extends Theme {}
6 | }
7 | 


--------------------------------------------------------------------------------
/src/state/router/router.selectors.ts:
--------------------------------------------------------------------------------
1 | import { State } from '../reducer'
2 | 
3 | export const selectLocation = (state: State) => state.router.location
4 | 
5 | export const selectPathname = (state: State) => state.router.location.pathname
6 | 


--------------------------------------------------------------------------------
/data/case-counts/owid/Turkmenistan.tsv:
--------------------------------------------------------------------------------
1 | # Data source: https://covid.ourworldindata.org/data/owid-covid-data.json
2 | # Data provenance: Our World in Data
3 | # License: CC-BY
4 | time	cases	deaths	hospitalized	icu	recovered
5 | 2021-02-28	0	0			
6 | 


--------------------------------------------------------------------------------
/src/types/glob-all.d.ts:
--------------------------------------------------------------------------------
 1 | export interface GlobAllOptions {
 2 |   nodir?: boolean
 3 | }
 4 | 
 5 | export declare class GlobAll {
 6 |   public static sync(paths: string, options?: GlobAllOptions): string[]
 7 | }
 8 | 
 9 | export default GlobAll
10 | 


--------------------------------------------------------------------------------
/.github/ISSUE_TEMPLATE/config.yml:
--------------------------------------------------------------------------------
1 | blank_issues_enabled: false
2 | contact_links:
3 |   - name: Ask a question
4 |     url: https://github.com/neherlab/covid19_scenarios/discussions
5 |     about: Ask questions and discuss with other community members
6 | 


--------------------------------------------------------------------------------
/src/styles/components/Footer.scss:
--------------------------------------------------------------------------------
 1 | @import '../variables';
 2 | 
 3 | .main-wrapper {
 4 |   min-height: 100vh;
 5 | }
 6 | 
 7 | .footer {
 8 |   bottom: -1px;
 9 |   min-height: 3em;
10 |   color: $gray-800;
11 |   background-color: $gray-200;
12 | }
13 | 


--------------------------------------------------------------------------------
/src/types/create-color.d.ts:
--------------------------------------------------------------------------------
1 | declare module 'create-color' {
2 |   export interface CreateColorOptions {
3 |     format: string
4 |   }
5 | 
6 |   export default function createColor(data: string | object | Array, options?: CreateColorOptions): string
7 | }
8 | 


--------------------------------------------------------------------------------
/src/helpers/copyToClipboard.ts:
--------------------------------------------------------------------------------
1 | export const copyToClipboard = (str: string) => {
2 |   const el = document.createElement('textarea')
3 |   el.value = str
4 |   document.body.append(el)
5 |   el.select()
6 |   document.execCommand('copy')
7 |   el.remove()
8 | }
9 | 


--------------------------------------------------------------------------------
/src/types/Intl.d.ts:
--------------------------------------------------------------------------------
1 | // merge missing fields for Intl.NumberFormatOptions
2 | // https://github.com/microsoft/TypeScript/issues/36533
3 | namespace Intl {
4 |   interface NumberFormatOptions {
5 |     notation?: string
6 |     compactDisplay?: string
7 |   }
8 | }
9 | 


--------------------------------------------------------------------------------
/src/state/ui/ui.actions.ts:
--------------------------------------------------------------------------------
1 | import actionCreatorFactory from 'typescript-fsa'
2 | 
3 | const action = actionCreatorFactory('UI')
4 | 
5 | export const printPreviewOpenTrigger = action('PRINT_PREVIEW_OPEN')
6 | 
7 | export const newTabOpenTrigger = action('NEW_TAB_OPEN')
8 | 


--------------------------------------------------------------------------------
/schemas/AgeGroup.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: AgeGroup
 3 | title: AgeGroup
 4 | 
 5 | type: string
 6 | enum:
 7 |   - 0-9
 8 |   - 10-19
 9 |   - 20-29
10 |   - 30-39
11 |   - 40-49
12 |   - 50-59
13 |   - 60-69
14 |   - 70-79
15 |   - 80+
16 | 


--------------------------------------------------------------------------------
/src/components/Main/Controls/filenames.ts:
--------------------------------------------------------------------------------
1 | export const FILENAME_PARAMS = 'c19s.params.json'
2 | export const FILENAME_RESULTS_SUMMARY = 'c19s.results.summary.tsv'
3 | export const FILENAME_RESULTS_DETAILED = 'c19s.results.detailed.tsv'
4 | export const FILENAME_ZIP = 'c19s.zip'
5 | 


--------------------------------------------------------------------------------
/lib/clear.js:
--------------------------------------------------------------------------------
1 | // Taken from jest:
2 | // https://github.com/facebook/jest/blob/v19.0.2/packages/jest-cli/src/constants.js#L15
3 | const isWindows = process.platform === 'win32'
4 | const CLEAR = isWindows ? '\u001Bc' : '\u001B[2J\u001B[3J\u001B[H'
5 | 
6 | process.stdout.write(CLEAR)
7 | 


--------------------------------------------------------------------------------
/src/helpers/getOrThrow.ts:
--------------------------------------------------------------------------------
1 | export function getOrThrow<K extends string, V>(map: Map<K, V>, key: K): V {
2 |   const value = map.get(key)
3 |   if (!value) {
4 |     throw new Error(`Value under key \`${key}\` was expected, but not found in the Map`)
5 |   }
6 |   return value
7 | }
8 | 


--------------------------------------------------------------------------------
/config/dotenv/index.js:
--------------------------------------------------------------------------------
 1 | const path = require('path')
 2 | 
 3 | const dotenv = require('dotenv')
 4 | 
 5 | const { findModuleRoot } = require('../../lib/findModuleRoot')
 6 | 
 7 | const { moduleRoot } = findModuleRoot()
 8 | 
 9 | dotenv.config({ path: path.join(moduleRoot, '.env') })
10 | 


--------------------------------------------------------------------------------
/src/styles/animate.scss:
--------------------------------------------------------------------------------
1 | /* stylelint-disable */
2 | 
3 | @import '~animate.css/source/_base.css';
4 | @import '~animate.css/source/_vars.css';
5 | @import '~animate.css/source/fading_entrances/fadeIn.css';
6 | @import '~animate.css/source/fading_exits/fadeOut.css';
7 | 
8 | /* stylelint-enable */
9 | 


--------------------------------------------------------------------------------
/src/types/svg-module.d.ts:
--------------------------------------------------------------------------------
1 | declare module '*.svg' {
2 |   import type { PureComponent, HTMLProps, SVGProps } from 'react'
3 | 
4 |   declare const url: string
5 |   declare class SVG extends PureComponent<SVGProps<SVGElement>> {}
6 |   export { SVG as ReactComponent }
7 |   export default url
8 | }
9 | 


--------------------------------------------------------------------------------
/src/styles/components/Popover.scss:
--------------------------------------------------------------------------------
 1 | @import '../variables';
 2 | 
 3 | .nl-popover {
 4 |   display: flex;
 5 | 
 6 |   > div:nth-of-type(2) {
 7 |     z-index: 2000;
 8 |     min-width: 276px;
 9 |     background-color: $white;
10 |     box-shadow: 0 0.25rem 0.5rem rgba(0, 0, 0, 0.2);
11 |   }
12 | }
13 | 


--------------------------------------------------------------------------------
/.gitignore:
--------------------------------------------------------------------------------
 1 | *.pyc
 2 | *.swp
 3 | *log
 4 | .DS_Store
 5 | \.build
 6 | \.cache
 7 | \.env
 8 | \.idea
 9 | \.output
10 | \.reports
11 | \.vscode
12 | cypress/screenshots
13 | cypress/videos
14 | data/generated
15 | data/parsers.log
16 | data/raw_data
17 | node_modules
18 | src/.generated/latest
19 | 
20 | .next
21 | 


--------------------------------------------------------------------------------
/config/jest/mocks/mockReactI18next.js:
--------------------------------------------------------------------------------
 1 | import { noop } from 'lodash'
 2 | 
 3 | const useMock = [(k) => k, {}]
 4 | useMock.t = (k) => k
 5 | useMock.i18n = {}
 6 | 
 7 | export const useTranslation = () => useMock
 8 | 
 9 | export const initReactI18next = {
10 |   type: '3rdParty',
11 |   init: noop,
12 | }
13 | 


--------------------------------------------------------------------------------
/lib/findModuleRoot.d.ts:
--------------------------------------------------------------------------------
1 | import { JSONSchemaForNPMPackageJsonFiles } from '@schemastore/package'
2 | 
3 | export interface FindModuleRootResult {
4 |   moduleRoot: string
5 |   pkg: JSONSchemaForNPMPackageJsonFiles
6 | }
7 | 
8 | export declare function findModuleRoot(maxDepth: number = 10): FindModuleRootResult
9 | 


--------------------------------------------------------------------------------
/.editorconfig:
--------------------------------------------------------------------------------
 1 | root = true
 2 | 
 3 | [*]
 4 | charset = utf-8
 5 | end_of_line = lf
 6 | indent_size = 2
 7 | indent_style = space
 8 | insert_final_newline = true
 9 | max_line_length = 120
10 | trim_trailing_whitespace = true
11 | 
12 | [*.md]
13 | trim_trailing_whitespace = false
14 | [*py]
15 | indent_size = 4
16 | 


--------------------------------------------------------------------------------
/schemas/Integer.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: Integer
 3 | title: Integer
 4 | 
 5 | # This is necessary to avoid discrepancies in current implementations
 6 | # https://json-schema.org/understanding-json-schema/reference/numeric.html#id4
 7 | 
 8 | type: integer
 9 | multipleOf: 1
10 | 


--------------------------------------------------------------------------------
/src/types/allow-methods.d.ts:
--------------------------------------------------------------------------------
1 | import { RequestHandler } from 'express'
2 | 
3 | type HttpMethod = 'GET' | 'HEAD' | 'POST' | 'PUT' | 'DELETE' | 'CONNECT' | 'OPTIONS' | 'TRACE' | 'PATCH'
4 | 
5 | declare function allowMethods(methods: HttpMethod[], errorMessage?: string): RequestHandler
6 | 
7 | export default allowMethods
8 | 


--------------------------------------------------------------------------------
/schemas/ScenarioArray.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: ScenarioArray
 3 | title: ScenarioArray
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - all
11 | 
12 | properties:
13 |   all:
14 |     type: array
15 |     items:
16 |       $ref: 'ScenarioData#'
17 | 


--------------------------------------------------------------------------------
/src/io/encoding/v1/encode.ts:
--------------------------------------------------------------------------------
 1 | import jsurl from 'jsurl'
 2 | 
 3 | export function encode(obj: Record<string, unknown>): string {
 4 |   return jsurl.stringify(obj)
 5 | }
 6 | 
 7 | export function decode(str: string) {
 8 |   return jsurl.parse(str) as Record<string, unknown>
 9 | }
10 | 
11 | export default { encode, decode }
12 | 


--------------------------------------------------------------------------------
/config/next/lib/CustomWebpackConfig.ts:
--------------------------------------------------------------------------------
1 | import { NextConfig, NextWebpackOptions } from 'next'
2 | import { WebpackOptions } from 'webpack/declarations/WebpackOptions'
3 | 
4 | export type CustomWebpackConfig = (
5 |   nextConfig: NextConfig,
6 |   webpackConfig: WebpackOptions,
7 |   options: NextWebpackOptions,
8 | ) => WebpackOptions
9 | 


--------------------------------------------------------------------------------
/config/next/withWorker.ts:
--------------------------------------------------------------------------------
1 | import type { NextConfig } from 'next'
2 | import WorkerPlugin from 'worker-plugin'
3 | 
4 | import { addWebpackPlugin } from './lib/addWebpackPlugin'
5 | 
6 | export default function withWorker(nextConfig: NextConfig) {
7 |   return addWebpackPlugin(nextConfig, new WorkerPlugin({ globalObject: 'self' }))
8 | }
9 | 


--------------------------------------------------------------------------------
/schemas/CaseCountsArray.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: CaseCountsArray
 3 | title: CaseCountsArray
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - all
11 | 
12 | properties:
13 |   all:
14 |     type: array
15 |     items:
16 |       $ref: 'CaseCountsData#'
17 | 


--------------------------------------------------------------------------------
/.eslintignore:
--------------------------------------------------------------------------------
 1 | 3rdparty
 2 | \.build
 3 | \.cache
 4 | \.circleci
 5 | \.env
 6 | \.git
 7 | \.github
 8 | \.github
 9 | \.idea
10 | \.ignore
11 | \.reports
12 | \.vscode
13 | \.vscode
14 | cypress
15 | data
16 | node_modules
17 | public
18 | schemas
19 | src/.generated
20 | src/assets
21 | src/i18n/resources
22 | styles
23 | tsconfig.json
24 | 


--------------------------------------------------------------------------------
/src/components/Wrappers/Popover.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import Popover from 'react-awesome-popover'
 4 | 
 5 | const WrappedPopover = (rest: Popover.PopoverProps) => (
 6 |   <Popover className="nl-popover" overlayColor="none" arrowProps={{ className: 'd-none' }} {...rest} />
 7 | )
 8 | 
 9 | export default WrappedPopover
10 | 


--------------------------------------------------------------------------------
/src/state/algorithm/algorithm.state.ts:
--------------------------------------------------------------------------------
 1 | import { AlgorithmResult } from '../../algorithms/types/Result.types'
 2 | 
 3 | export interface AlgorithmState {
 4 |   isRunning: boolean
 5 |   result?: AlgorithmResult
 6 | }
 7 | 
 8 | export const defaultAlgorithmState: AlgorithmState = {
 9 |   isRunning: false,
10 |   result: undefined,
11 | }
12 | 


--------------------------------------------------------------------------------
/src/types/ajv-i18n.d.ts:
--------------------------------------------------------------------------------
 1 | import { ErrorObject } from 'ajv'
 2 | 
 3 | export declare type AjvI18nLocalizeFunction = (errors: ErrorObject[]) => void
 4 | 
 5 | export declare interface AjvI18n {
 6 |   [key: string]: AjvI18nLocalizeFunction
 7 | }
 8 | 
 9 | declare const ajvLocalizers = {} as AjvI18n
10 | 
11 | export default ajvLocalizers
12 | 


--------------------------------------------------------------------------------
/src/types/assets.d.ts:
--------------------------------------------------------------------------------
 1 | declare module '*.txt' {
 2 |   declare const content: string
 3 |   export default content
 4 | }
 5 | 
 6 | declare module '*.csv' {
 7 |   declare const content: string
 8 |   export default content
 9 | }
10 | 
11 | declare module '*.tsv' {
12 |   declare const content: string
13 |   export default content
14 | }
15 | 


--------------------------------------------------------------------------------
/data/case-counts/india/IND-Goa***.tsv:
--------------------------------------------------------------------------------
1 | # Data source: https://api.rootnet.in/covid19-in/stats/daily
2 | # Data provenance: https://github.com/amodm/api-covid19-in
3 | # License: Scraped from Ministry of Health and Family Welfare plus other sources, no clear license
4 | time	cases	deaths	hospitalized	icu	recovered
5 | 2021-09-16	175088	3289			
6 | 


--------------------------------------------------------------------------------
/data/case-counts/india/IND-Punjab***.tsv:
--------------------------------------------------------------------------------
1 | # Data source: https://api.rootnet.in/covid19-in/stats/daily
2 | # Data provenance: https://github.com/amodm/api-covid19-in
3 | # License: Scraped from Ministry of Health and Family Welfare plus other sources, no clear license
4 | time	cases	deaths	hospitalized	icu	recovered
5 | 2020-11-15	140605	4428			
6 | 


--------------------------------------------------------------------------------
/src/components/Main/PrintPreview/PrintDisclaimer.mdx:
--------------------------------------------------------------------------------
1 | This tool is not a medical predictor, and should be used for informational and research purposes only. Please carefully
2 | consider the parameters you choose. Interpret and use the simulated results responsibly. Authors are not liable for any
3 | direct or indirect consequences of this usage.
4 | 


--------------------------------------------------------------------------------
/config/jest/mocks/mockPopperJS.js:
--------------------------------------------------------------------------------
 1 | // mock popper.js (reactstrap dependency via react-popper)
 2 | // see: https://github.com/popperjs/popper-core/issues/478#issuecomment-341494703
 3 | 
 4 | export default class {
 5 |   constructor() {
 6 |     return {
 7 |       destroy: () => null,
 8 |       scheduleUpdate: () => null,
 9 |     }
10 |   }
11 | }
12 | 


--------------------------------------------------------------------------------
/data/case-counts/india/IND-Chandigarh***.tsv:
--------------------------------------------------------------------------------
1 | # Data source: https://api.rootnet.in/covid19-in/stats/daily
2 | # Data provenance: https://github.com/amodm/api-covid19-in
3 | # License: Scraped from Ministry of Health and Family Welfare plus other sources, no clear license
4 | time	cases	deaths	hospitalized	icu	recovered
5 | 2020-11-15	15636	246			
6 | 


--------------------------------------------------------------------------------
/data/case-counts/india/IND-Uttarakhand***.tsv:
--------------------------------------------------------------------------------
1 | # Data source: https://api.rootnet.in/covid19-in/stats/daily
2 | # Data provenance: https://github.com/amodm/api-covid19-in
3 | # License: Scraped from Ministry of Health and Family Welfare plus other sources, no clear license
4 | time	cases	deaths	hospitalized	icu	recovered
5 | 2021-02-21	97031	1686			
6 | 


--------------------------------------------------------------------------------
/src/styles/components/Loading.scss:
--------------------------------------------------------------------------------
 1 | .loading-page {
 2 |   position: fixed;
 3 |   top: 0;
 4 |   right: 0;
 5 |   bottom: 0;
 6 |   left: 0;
 7 |   display: flex;
 8 |   flex-direction: column;
 9 |   align-items: center;
10 | 
11 |   > .spinner-border {
12 |     width: 6rem;
13 |     height: 6rem;
14 |     animation-duration: 1.5s;
15 |   }
16 | }
17 | 


--------------------------------------------------------------------------------
/.prettierignore:
--------------------------------------------------------------------------------
 1 | *.lock
 2 | *.log
 3 | \.build
 4 | \.cache
 5 | \.editorconfig
 6 | \.env
 7 | \.git
 8 | \.gitignore
 9 | \.ignore
10 | \.prettierignore
11 | \.reports
12 | \.vscode
13 | data/**/*.csv
14 | data/**/*.json
15 | data/**/*.tsv
16 | data/case-counts
17 | data/hospital-data
18 | node_modules
19 | src/.generated
20 | src/assets/data/**/*.json
21 | 


--------------------------------------------------------------------------------
/schemas/AgeDistributionArray.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: AgeDistributionArray
 3 | title: AgeDistributionArray
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - all
11 | 
12 | properties:
13 |   all:
14 |     type: array
15 |     items:
16 |       $ref: 'AgeDistributionData#'
17 | 


--------------------------------------------------------------------------------
/schemas/IntegerPositive.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: IntegerPositive
 3 | title: IntegerPositive
 4 | 
 5 | # This is necessary to avoid discrepancies in current implementations
 6 | # https://json-schema.org/understanding-json-schema/reference/numeric.html#id4
 7 | 
 8 | type: integer
 9 | multipleOf: 1
10 | minimum: 1
11 | 


--------------------------------------------------------------------------------
/src/state/error/error.actions.ts:
--------------------------------------------------------------------------------
 1 | import actionCreatorFactory from 'typescript-fsa'
 2 | 
 3 | const action = actionCreatorFactory('ERROR')
 4 | 
 5 | export interface GenericErrorParams {
 6 |   error: Error
 7 | }
 8 | 
 9 | export const errorAdd = action<GenericErrorParams>('ERROR_ADD')
10 | 
11 | export const errorDismiss = action<unknown>('ERROR_DISMISS')
12 | 


--------------------------------------------------------------------------------
/schemas/IntegerNonNegative.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: IntegerNonNegative
 3 | title: IntegerNonNegative
 4 | 
 5 | # This is necessary to avoid discrepancies in current implementations
 6 | # https://json-schema.org/understanding-json-schema/reference/numeric.html#id4
 7 | 
 8 | type: integer
 9 | multipleOf: 1
10 | minimum: 0
11 | 


--------------------------------------------------------------------------------
/schemas/ScenarioData.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: ScenarioData
 3 | title: ScenarioData
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - name
11 |   - data
12 | 
13 | properties:
14 |   name:
15 |     type: string
16 |     minLength: 1
17 | 
18 |   data:
19 |     $ref: 'ScenarioDatum#'
20 | 


--------------------------------------------------------------------------------
/src/types/size-plugin.d.ts:
--------------------------------------------------------------------------------
 1 | export interface SizePluginOptions {
 2 |   pattern?: string
 3 |   exclude?: string
 4 |   filename?: string
 5 |   publish?: boolean
 6 |   writeFile?: boolean
 7 |   stripHash?(filename: string): string
 8 | }
 9 | 
10 | declare class SizePlugin {
11 |   constructor(options: SizePluginOptions)
12 | }
13 | 
14 | export default SizePlugin
15 | 


--------------------------------------------------------------------------------
/schemas/SeverityDistributionArray.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: SeverityDistributionArray
 3 | title: SeverityDistributionArray
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - all
11 | 
12 | properties:
13 |   all:
14 |     type: array
15 |     items:
16 |       $ref: 'SeverityDistributionData#'
17 | 


--------------------------------------------------------------------------------
/src/algorithms/utils/exceptions.ts:
--------------------------------------------------------------------------------
 1 | export enum ProcessingErrorCode {
 2 |   MissingTimeField,
 3 |   InvalidField,
 4 | }
 5 | 
 6 | /**
 7 |  * A custom exception thrown during data file parsing.
 8 |  */
 9 | export class ProcessingError extends Error {
10 |   constructor(readonly errorCode: ProcessingErrorCode, message?: string) {
11 |     super(message)
12 |   }
13 | }
14 | 


--------------------------------------------------------------------------------
/src/helpers/getCopyrightYearRange.ts:
--------------------------------------------------------------------------------
 1 | import { COPYRIGHT_YEAR_START } from 'src/constants'
 2 | 
 3 | export function getCopyrightYearRange() {
 4 |   const currentYear = new Date().getFullYear()
 5 | 
 6 |   if (COPYRIGHT_YEAR_START < currentYear) {
 7 |     return `${COPYRIGHT_YEAR_START}-${currentYear}`
 8 |   }
 9 | 
10 |   return COPYRIGHT_YEAR_START.toString()
11 | }
12 | 


--------------------------------------------------------------------------------
/src/helpers/useTranslationSafe.ts:
--------------------------------------------------------------------------------
 1 | import { Namespace, useTranslation, UseTranslationOptions } from 'react-i18next'
 2 | 
 3 | export function useTranslationSafe(ns?: Namespace, options?: UseTranslationOptions) {
 4 |   const response = useTranslation()
 5 |   function t(key: string) {
 6 |     return response.t(key) ?? key
 7 |   }
 8 |   return { ...response, t }
 9 | }
10 | 


--------------------------------------------------------------------------------
/src/types/threads-plugin.d.ts:
--------------------------------------------------------------------------------
 1 | import webpack from 'webpack'
 2 | 
 3 | export interface ThreadsPluginOptions {
 4 |   globalObject?: boolean | string
 5 |   plugins?: Array<string | webpack.Plugin>
 6 |   target?: string
 7 | }
 8 | 
 9 | declare class WorkerPlugin extends webpack.Plugin {
10 |   constructor(options?: ThreadsPluginOptions)
11 | }
12 | 
13 | export default WorkerPlugin
14 | 


--------------------------------------------------------------------------------
/src/io/serialization/fromUrl.ts:
--------------------------------------------------------------------------------
 1 | import { ScenarioParameters } from '../../algorithms/types/Param.types'
 2 | 
 3 | import { decode } from '../encoding/decode'
 4 | 
 5 | import { deserialize } from './deserialize'
 6 | 
 7 | export function fromUrl(url: string): ScenarioParameters {
 8 |   const obj = decode(url)
 9 |   const str = JSON.stringify(obj)
10 |   return deserialize(str)
11 | }
12 | 


--------------------------------------------------------------------------------
/schemas/AgeDistributionDatum.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: AgeDistributionDatum
 3 | title: AgeDistributionDatum
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - ageGroup
11 |   - population
12 | 
13 | properties:
14 |   ageGroup:
15 |     $ref: 'AgeGroup#'
16 | 
17 |   population:
18 |     $ref: 'IntegerNonNegative#'
19 | 


--------------------------------------------------------------------------------
/schemas/ScenarioDatumMitigation.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: ScenarioDatumMitigation
 3 | title: ScenarioDatumMitigation
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - mitigationIntervals
11 | 
12 | properties:
13 |   mitigationIntervals:
14 |     type: array
15 |     items:
16 |       $ref: 'MitigationInterval#'
17 | 


--------------------------------------------------------------------------------
/src/state/algorithm/algorithm.selectors.ts:
--------------------------------------------------------------------------------
 1 | import { isNil } from 'lodash'
 2 | 
 3 | import { State } from '../reducer'
 4 | 
 5 | export const selectIsRunning = (state: State) => state.algorithm.isRunning
 6 | 
 7 | export const selectResult = (state: State) => state.algorithm.result
 8 | 
 9 | export const selectHasResult = (state: State): boolean => !isNil(state.algorithm.result?.trajectory)
10 | 


--------------------------------------------------------------------------------
/src/components/Main/PrintPreview/dateFormat.ts:
--------------------------------------------------------------------------------
 1 | import moment from 'moment'
 2 | 
 3 | export function dateFormat(date: Date) {
 4 |   return moment(date).format('MMM DD YYYY') // eslint-disable-line i18next/no-literal-string
 5 | }
 6 | 
 7 | export function dateTimeFormat(date: Date) {
 8 |   return moment(date).format('MMM DD YYYY, hh:mm A') // eslint-disable-line i18next/no-literal-string
 9 | }
10 | 


--------------------------------------------------------------------------------
/src/io/encoding/encode.ts:
--------------------------------------------------------------------------------
 1 | import queryString from 'query-string'
 2 | 
 3 | import { URL_ENCODER_LATEST, URL_ENCODER_VERSION_LATEST } from './versioning'
 4 | 
 5 | export function encode(obj: Record<string, unknown>) {
 6 |   const q = URL_ENCODER_LATEST.encode(obj)
 7 |   const v = URL_ENCODER_VERSION_LATEST
 8 |   const query = queryString.stringify({ v, q })
 9 |   return `/?${query}`
10 | }
11 | 


--------------------------------------------------------------------------------
/3rdparty/__empty-module/package.json:
--------------------------------------------------------------------------------
1 | {
2 |   "name": "__empty-module",
3 |   "description": "You can link undesired dependencies to this module. For example, you may link known obsolete (json3), or unsafe (letf-pad) or unnecessary (some polyfills) modules and they will resolve to an empty module.",
4 |   "version": "0.0.0",
5 |   "main": "index.js",
6 |   "license": "UNLICENSED",
7 |   "private": true
8 | }
9 | 


--------------------------------------------------------------------------------
/config/next/withEnvironment.ts:
--------------------------------------------------------------------------------
 1 | import { NextConfig } from 'next'
 2 | import Webpack from 'webpack'
 3 | import { addWebpackPlugin } from './lib/addWebpackPlugin'
 4 | 
 5 | const getWithEnvironment = (envs: string[] | { [key: string]: string }) => (nextConfig: NextConfig) => {
 6 |   return addWebpackPlugin(nextConfig, new Webpack.EnvironmentPlugin(envs))
 7 | }
 8 | 
 9 | export default getWithEnvironment
10 | 


--------------------------------------------------------------------------------
/schemas/CaseCountsData.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: CaseCountsData
 3 | title: CaseCountsData
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - name
11 |   - data
12 | 
13 | properties:
14 |   name:
15 |     type: string
16 |     minLength: 1
17 | 
18 |   data:
19 |     type: array
20 |     items:
21 |       $ref: 'CaseCountsDatum#'
22 | 


--------------------------------------------------------------------------------
/src/types/stylelint-bare-webpack-plugin.d.ts:
--------------------------------------------------------------------------------
 1 | import { Formatter } from 'stylelint'
 2 | 
 3 | export interface StylelintBarePluginOptions {
 4 |   files?: string
 5 |   emitErrors?: boolean
 6 |   failOnError?: boolean
 7 |   formatter?: Formatter
 8 | }
 9 | 
10 | declare class StylelintBarePlugin {
11 |   constructor(options: StylelintBarePluginOptions)
12 | }
13 | 
14 | export default StylelintBarePlugin
15 | 


--------------------------------------------------------------------------------
/src/io/serialization/toUrl.ts:
--------------------------------------------------------------------------------
 1 | import { ScenarioParameters } from '../../algorithms/types/Param.types'
 2 | 
 3 | import { encode } from '../encoding/encode'
 4 | 
 5 | import { serialize } from './serialize'
 6 | 
 7 | export function toUrl(data: ScenarioParameters): string {
 8 |   const serialized = serialize(data)
 9 |   const obj = JSON.parse(serialized) as Record<string, unknown>
10 |   return encode(obj)
11 | }
12 | 


--------------------------------------------------------------------------------
/config/next/withRaw.ts:
--------------------------------------------------------------------------------
 1 | import type { NextConfig } from 'next'
 2 | 
 3 | import { addWebpackLoader } from './lib/addWebpackLoader'
 4 | 
 5 | export default function withRaw(nextConfig: NextConfig) {
 6 |   return addWebpackLoader(nextConfig, (webpackConfig, { dev }) => ({
 7 |     test: /\.(txt|csv|tsv|fasta)$/i,
 8 |     use: [
 9 |       {
10 |         loader: 'raw-loader',
11 |       },
12 |     ],
13 |   }))
14 | }
15 | 


--------------------------------------------------------------------------------
/schemas/PercentageRange.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: PercentageRange
 3 | title: PercentageRange
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - begin
11 |   - end
12 | 
13 | properties:
14 |   begin:
15 |     type: number
16 |     minimum: 0
17 |     maximum:
18 |       $data: '1/end'
19 | 
20 |   end:
21 |     type: number
22 |     maximum: 100
23 | 


--------------------------------------------------------------------------------
/data/Pipfile:
--------------------------------------------------------------------------------
 1 | [[source]]
 2 | name = "pypi"
 3 | url = "https://pypi.org/simple"
 4 | verify_ssl = true
 5 | 
 6 | [dev-packages]
 7 | 
 8 | [packages]
 9 | numpy = "*"
10 | scipy = "*"
11 | matplotlib = "*"
12 | requests = "*"
13 | xlrd = "*"
14 | schemapi = {editable = true,git = "https://github.com/altair-viz/schemapi.git"}
15 | ipython = "*"
16 | pandas = "*"
17 | pyyaml = "*"
18 | 
19 | [requires]
20 | python_version = "3.8"
21 | 


--------------------------------------------------------------------------------
/schemas/AgeDistributionData.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: AgeDistributionData
 3 | title: AgeDistributionData
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - name
11 |   - data
12 | 
13 | properties:
14 |   name:
15 |     type: string
16 |     minLength: 1
17 | 
18 |   data:
19 |     type: array
20 |     items:
21 |       $ref: 'AgeDistributionDatum#'
22 | 


--------------------------------------------------------------------------------
/schemas/NumericRangeNonNegative.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: NumericRangeNonNegative
 3 | title: NumericRangeNonNegative
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - begin
11 |   - end
12 | 
13 | properties:
14 |   begin:
15 |     type: number
16 |     minimum: 0
17 |     maximum:
18 |       $data: '1/end'
19 | 
20 |   end:
21 |     type: number
22 | 


--------------------------------------------------------------------------------
/src/styles/components/LanguageSwitcher.scss:
--------------------------------------------------------------------------------
 1 | @import '../variables';
 2 | 
 3 | .language-switcher {
 4 |   .language-switcher-menu.dropdown-menu {
 5 |     background-color: $body-background;
 6 |   }
 7 | 
 8 |   .language-switcher-flag {
 9 |     width: 20px;
10 |     height: 20px;
11 |     margin-bottom: 5px;
12 |     background-size: cover;
13 |     border-radius: 2px;
14 |     box-shadow: 1px 1px 1px 1px #2222;
15 |   }
16 | }
17 | 


--------------------------------------------------------------------------------
/data/case-counts/india/IND-Bihar****.tsv:
--------------------------------------------------------------------------------
1 | # Data source: https://api.rootnet.in/covid19-in/stats/daily
2 | # Data provenance: https://github.com/amodm/api-covid19-in
3 | # License: Scraped from Ministry of Health and Family Welfare plus other sources, no clear license
4 | time	cases	deaths	hospitalized	icu	recovered
5 | 2021-06-09	715179	9429			
6 | 2021-06-10	715730	9452			
7 | 2021-06-11	715730	9452			
8 | 2021-06-12	716296	9466			
9 | 


--------------------------------------------------------------------------------
/src/components/Form/FormDropdownOption.ts:
--------------------------------------------------------------------------------
 1 | export interface FormDropdownOption<ValueType extends string | number> {
 2 |   value: ValueType
 3 |   label: string
 4 | }
 5 | 
 6 | export function stringToOption(value: string): FormDropdownOption<string> {
 7 |   return { value, label: value }
 8 | }
 9 | 
10 | export function stringsToOptions(values: string[]): FormDropdownOption<string>[] {
11 |   return values.map(stringToOption)
12 | }
13 | 


--------------------------------------------------------------------------------
/data/case-counts/china/CHN-Xizang.tsv:
--------------------------------------------------------------------------------
 1 | # Data source: https://github.com/BlankerL/DXY-COVID-19-Data/raw/master/csv/DXYOverall.csv
 2 | # Data provenance: https://github.com/BlankerL/DXY-COVID-19-Data
 3 | # License: MIT
 4 | time	cases	deaths	hospitalized	icu	recovered
 5 | 2020-01-29	0	0			0
 6 | 2020-01-30	1	0			0
 7 | 2020-02-02	1	0			0
 8 | 2020-02-04	1	0			0
 9 | 2020-02-12	1	0			1
10 | 2020-02-13	1	0			1
11 | 2020-02-23	1	0			1
12 | 


--------------------------------------------------------------------------------
/schemas/SeverityDistributionData.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: SeverityDistributionData
 3 | title: SeverityDistributionData
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - name
11 |   - data
12 | 
13 | properties:
14 |   name:
15 |     type: string
16 |     minLength: 1
17 | 
18 |   data:
19 |     type: array
20 |     items:
21 |       $ref: 'SeverityDistributionDatum#'
22 | 


--------------------------------------------------------------------------------
/src/types/remark-rehype.d.ts:
--------------------------------------------------------------------------------
 1 | declare module 'remark-images' {
 2 |   const plugin: any
 3 |   export default plugin
 4 | }
 5 | 
 6 | declare module 'remark-math' {
 7 |   const plugin: any
 8 |   export default plugin
 9 | }
10 | 
11 | declare module '@silvenon/remark-smartypants' {
12 |   const plugin: any
13 |   export default plugin
14 | }
15 | 
16 | declare module 'rehype-katex' {
17 |   const plugin: any
18 |   export default plugin
19 | }
20 | 


--------------------------------------------------------------------------------
/src/styles/components/ErrorPage.scss:
--------------------------------------------------------------------------------
 1 | @import '../variables';
 2 | 
 3 | .h1-error {
 4 |   padding: 2rem;
 5 |   margin-bottom: 0;
 6 |   color: #fff;
 7 |   background-color: #a72a33;
 8 | }
 9 | 
10 | .h3-error {
11 |   margin-top: 50px;
12 | }
13 | 
14 | .error-container-dev {
15 |   padding: 10px;
16 |   margin-top: 0;
17 | }
18 | 
19 | .error-dev {
20 |   font-family: $font-family-monospace;
21 |   color: #ccc;
22 |   background-color: #222;
23 | }
24 | 


--------------------------------------------------------------------------------
/src/components/Main/ScenarioLoader/ScenarioLoaderUploadInstructionsText.mdx:
--------------------------------------------------------------------------------
1 | Here you can load your scenario parameters in JSON format into the simulator.
2 | 
3 | For a concrete example of a Scenario JSON File you may export any of the predefined scenarios using "Export"
4 | functionality in the simulator. For Scenario JSON File format reference, see JSON schema
5 | [Shareable.yml](https://github.com/neherlab/covid19_scenarios/blob/master/schemas/Shareable.yml).
6 | 


--------------------------------------------------------------------------------
/src/types/react-awesome-popover.d.ts:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | declare class Popover extends React.Component<Popover.PopoverProps> {}
 4 | 
 5 | declare namespace Popover {
 6 |   interface PopoverProps extends React.HTMLAttributes<HTMLElement> {
 7 |     placement?: string
 8 |     overlayColor?: string
 9 |     preventDefault?: boolean
10 |     stopPropagation?: boolean
11 |     arrowProps?: object
12 |   }
13 | }
14 | 
15 | export default Popover
16 | 


--------------------------------------------------------------------------------
/src/types/hot-module.d.ts:
--------------------------------------------------------------------------------
 1 | // Workaround for hot module replacement
 2 | interface NodeHotModule extends NodeModule {
 3 |   hot: {
 4 |     accept(dependency: string, callback: () => void | Promise<void>): void
 5 |     accept(errHandler?: (err: Error) => void | Promise<void>): void
 6 |     accept(path?: () => void, callback?: () => void | Promise<void>): void
 7 |     decline(): void
 8 |     dispose(callback: <T>(data: T) => void | Promise<void>): void
 9 |   }
10 | }
11 | 


--------------------------------------------------------------------------------
/postcss.config.js:
--------------------------------------------------------------------------------
 1 | require('./config/dotenv')
 2 | 
 3 | module.exports = {
 4 |   plugins: {
 5 |     'postcss-flexbugs-fixes': {},
 6 |     'postcss-preset-env': {
 7 |       stage: 2,
 8 |       features: {
 9 |         'custom-properties': false,
10 |         'postcss-custom-properties': { preserve: false },
11 |       },
12 |       autoprefixer: {
13 |         remove: false,
14 |         grid: 'autoplace',
15 |         flexbox: 'no-2009',
16 |       },
17 |     },
18 |   },
19 | }
20 | 


--------------------------------------------------------------------------------
/data/paths.py:
--------------------------------------------------------------------------------
 1 | import os
 2 | 
 3 | BASE_PATH = os.path.join(os.path.dirname(os.path.realpath(__file__)))
 4 | JSON_DIR = 'assets'
 5 | TSV_DIR = 'case-counts'
 6 | SOURCES_FILE = 'sources.json'
 7 | TMP_CASES = 'case_counts.json'
 8 | TMP_POPULATION = 'population.json'
 9 | TMP_SCENARIOS = "scenario_defaults.json"
10 | PARSERS_LOG_FILE = 'parsers.log'
11 | FIT_PARAMETERS = 'fit_parameters.json'
12 | SCHEMA_CASECOUNTS = '../schemas/CaseCounts.yml'
13 | SCHEMA_DIR = '../schemas/ScenarioArray.yml'
14 | 


--------------------------------------------------------------------------------
/docker/node-git-alpine/Dockerfile:
--------------------------------------------------------------------------------
 1 | FROM node:14.4.0-alpine3.11
 2 | 
 3 | ENV DOCKERIZE_VERSION v0.6.1
 4 | ENV DOCKERIZE_URL "https://github.com/jwilder/dockerize/releases/download/${DOCKERIZE_VERSION}/dockerize-alpine-linux-amd64-${DOCKERIZE_VERSION}.tar.gz"
 5 | 
 6 | RUN apk add --update --no-cache \
 7 |   curl \
 8 |   git \
 9 | > /dev/null
10 | 
11 | RUN curl -fsSL "${DOCKERIZE_URL}" | tar xfz - -C "/usr/local/bin/"
12 | 
13 | ENTRYPOINT ["docker-entrypoint.sh"]
14 | 
15 | CMD [ "node" ]
16 | 


--------------------------------------------------------------------------------
/src/components/Link/LinkExternal.tsx:
--------------------------------------------------------------------------------
 1 | import React, { PropsWithChildren } from 'react'
 2 | 
 3 | export interface LinkExternalProps extends React.HTMLProps<HTMLAnchorElement> {
 4 |   url?: string
 5 |   href?: string
 6 | }
 7 | 
 8 | export function LinkExternal({ url, href, children, ...restProps }: PropsWithChildren<LinkExternalProps>) {
 9 |   return (
10 |     <a target="_blank" rel="noopener noreferrer" href={url ?? href} {...restProps}>
11 |       {children}
12 |     </a>
13 |   )
14 | }
15 | 


--------------------------------------------------------------------------------
/.yarnrc:
--------------------------------------------------------------------------------
 1 | # Don't check for updates of yarn itself
 2 | disable-self-update-check true
 3 | 
 4 | # Install exact versions (not prefixed with '^')
 5 | save-prefix ""
 6 | 
 7 | # Don't run post-install scripts (for security reasons)
 8 | --install.ignore-scripts true
 9 | --add.ignore-scripts true
10 | --remove.ignore-scripts true
11 | 
12 | # Don't check Node version
13 | ignore-engines true
14 | 
15 | # Keep yarn cache locally for faster and more reproducible builds
16 | cache-folder ".cache/yarn"
17 | 


--------------------------------------------------------------------------------
/schemas/ScenarioDatumSimulation.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: ScenarioDatumSimulation
 3 | title: ScenarioDatumSimulation
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - simulationTimeRange
11 |   - numberStochasticRuns
12 | 
13 | properties:
14 |   simulationTimeRange:
15 |     $ref: 'DateRange#'
16 | 
17 |   numberStochasticRuns:
18 |     allOf:
19 |       - $ref: 'Integer#'
20 |       - minimum: 10
21 |         maximum: 100
22 | 


--------------------------------------------------------------------------------
/src/types/redux-immutable-state-invariant.d.ts:
--------------------------------------------------------------------------------
 1 | import Redux from 'redux'
 2 | 
 3 | export declare interface ImmutableStateInvariantMiddlewareOptions {
 4 |   isImmutable?: (value: any) => boolean
 5 |   ignore?: string[]
 6 | }
 7 | 
 8 | export declare type ImmutableStateInvariantMiddleware = (
 9 |   options?: ImmutableStateInvariantMiddlewareOptions,
10 | ) => Redux.Middleware
11 | 
12 | declare const immutableStateInvariant: ImmutableStateInvariantMiddleware
13 | 
14 | export default immutableStateInvariant
15 | 


--------------------------------------------------------------------------------
/config/next/withoutMinification.ts:
--------------------------------------------------------------------------------
 1 | import { NextConfig } from 'next'
 2 | import { addWebpackConfig } from './lib/addWebpackConfig'
 3 | 
 4 | export default function withoutMinification(nextConfig: NextConfig) {
 5 |   return addWebpackConfig(nextConfig, (nextConfig, webpackConfig, options) => {
 6 |     if (webpackConfig.optimization) {
 7 |       webpackConfig.optimization.minimizer = []
 8 |     } else {
 9 |       webpackConfig.optimization = { minimizer: [] }
10 |     }
11 |     return webpackConfig
12 |   })
13 | }
14 | 


--------------------------------------------------------------------------------
/src/io/encoding/errors.ts:
--------------------------------------------------------------------------------
 1 | import { ErrorArray } from '../../helpers/ErrorArray'
 2 | 
 3 | export class URLDecodingError extends ErrorArray {}
 4 | 
 5 | export class ErrorURLDecoderVersionInvalid extends URLDecodingError {
 6 |   public urlVer: string
 7 | 
 8 |   public constructor(urlVer: string, urlEncoderVersions: string[]) {
 9 |     super(`when serializing expected \`v\` to be one of \`[${urlEncoderVersions.join(', ')}]\`, but received: ${urlVer}`) // prettier-ignore
10 |     this.urlVer = urlVer
11 |   }
12 | }
13 | 


--------------------------------------------------------------------------------
/src/components/Layout/ColCustom.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import { Col } from 'reactstrap'
 4 | import type { ColProps as ReactstrapColProps } from 'reactstrap/lib/Col'
 5 | 
 6 | export interface ColProps extends Omit<ReactstrapColProps, 'ref'> {
 7 |   readonly xxl?: number
 8 | }
 9 | 
10 | function ColCustom({ ...restProps }: ColProps) {
11 |   return <Col widths={['xs', 'sm', 'md', 'lg', 'xl', 'xxl']} {...restProps} /> // eslint-disable-line i18next/no-literal-string
12 | }
13 | 
14 | export { ColCustom }
15 | 


--------------------------------------------------------------------------------
/src/components/Layout/MdxWrapper.tsx:
--------------------------------------------------------------------------------
 1 | import React, { HTMLProps } from 'react'
 2 | 
 3 | import classNames from 'classnames'
 4 | import { Row, Col } from 'reactstrap'
 5 | 
 6 | export function MdxWrapper<T extends HTMLProps<HTMLDivElement>>(props: T) {
 7 |   const { children, className } = props
 8 |   return (
 9 |     <div {...props} className={classNames(className, 'container container-fluid mdx-wrapper my-2 px-3 py-3')}>
10 |       <Row>
11 |         <Col>{children}</Col>
12 |       </Row>
13 |     </div>
14 |   )
15 | }
16 | 


--------------------------------------------------------------------------------
/schemas/MitigationInterval.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: MitigationInterval
 3 | title: MitigationInterval
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - name
11 |   - color
12 |   - timeRange
13 |   - transmissionReduction
14 | 
15 | properties:
16 |   name:
17 |     type: string
18 |     minLength: 1
19 | 
20 |   color:
21 |     $ref: 'ColorHex#'
22 | 
23 |   timeRange:
24 |     $ref: 'DateRange#'
25 | 
26 |   transmissionReduction:
27 |     $ref: 'PercentageRange#'
28 | 


--------------------------------------------------------------------------------
/src/components/Form/FormLabel.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import HelpLabel from './HelpLabel'
 4 | 
 5 | export interface LabelWithHelpButtonProps {
 6 |   identifier: string
 7 |   label: string | React.ReactNode
 8 |   help?: string | React.ReactNode
 9 | }
10 | 
11 | export default function FormLabel({ identifier, label, help }: LabelWithHelpButtonProps) {
12 |   return (
13 |     <label htmlFor={identifier} className="d-flex">
14 |       <HelpLabel identifier={identifier} label={label} help={help} />
15 |     </label>
16 |   )
17 | }
18 | 


--------------------------------------------------------------------------------
/src/components/Updates/UpdatesPage.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import { Col, Container, Row } from 'reactstrap'
 4 | import { useTranslation } from 'react-i18next'
 5 | 
 6 | import UpdatesContent from './UpdatesContent.md'
 7 | 
 8 | export function UpdatesPage() {
 9 |   const { t } = useTranslation()
10 | 
11 |   return (
12 |     <Container>
13 |       <Row>
14 |         <Col>
15 |           <h1>{t('Updates to model')}</h1>
16 |           <UpdatesContent />
17 |         </Col>
18 |       </Row>
19 |     </Container>
20 |   )
21 | }
22 | 


--------------------------------------------------------------------------------
/src/io/parsingCsv/errors.ts:
--------------------------------------------------------------------------------
 1 | import { appendDash } from '../../helpers/appendDash'
 2 | import { ErrorArray } from '../../helpers/ErrorArray'
 3 | 
 4 | export class CSVParserError extends ErrorArray {
 5 |   public readonly errors?: string[]
 6 | }
 7 | 
 8 | export class CSVParserErrorCSVSyntaxInvalid extends CSVParserError {
 9 |   public readonly errors: string[]
10 | 
11 |   public constructor(errors: string[]) {
12 |     super(`when parsing CSV: syntax error:\n${errors?.map(appendDash).join('\n')}`)
13 |     this.errors = errors
14 |   }
15 | }
16 | 


--------------------------------------------------------------------------------
/src/styles/components/ModalButtonExport.scss:
--------------------------------------------------------------------------------
 1 | @import '../variables';
 2 | 
 3 | .modal-dialog.export-modal {
 4 |   max-width: 600px;
 5 | }
 6 | 
 7 | .export-file-icon-container {
 8 |   flex: 0 0 50px;
 9 |   margin: auto;
10 |   min-width: 50px;
11 |   max-width: 50px;
12 | 
13 |   svg {
14 |     filter: drop-shadow(3px 3px 3px rgba(0, 0, 0, 0.4));
15 |   }
16 | }
17 | 
18 | .btn-download svg {
19 |   fill: $gray-600;
20 |   filter: drop-shadow(2px 2px 2px rgba(0, 0, 0, 0.4));
21 | }
22 | 
23 | .export-file-filename {
24 |   font-size: 1em;
25 | }
26 | 


--------------------------------------------------------------------------------
/config/next/withExtraWatch.ts:
--------------------------------------------------------------------------------
 1 | import type { NextConfig } from 'next'
 2 | import ExtraWatchWebpackPlugin from 'extra-watch-webpack-plugin'
 3 | 
 4 | import { addWebpackPlugin } from './lib/addWebpackPlugin'
 5 | 
 6 | export interface WithExtraWatchOptions {
 7 |   files: string[]
 8 |   dirs: string[]
 9 | }
10 | 
11 | const getWithExtraWatch = ({ files, dirs }: WithExtraWatchOptions) => (nextConfig: NextConfig) => {
12 |   return addWebpackPlugin(nextConfig, new ExtraWatchWebpackPlugin({ files, dirs }))
13 | }
14 | 
15 | export default getWithExtraWatch
16 | 


--------------------------------------------------------------------------------
/src/initialize.ts:
--------------------------------------------------------------------------------
 1 | import type { Router } from 'next/router'
 2 | 
 3 | import { configureStore } from 'src/state/store'
 4 | import { setLocale } from 'src/state/settings/settings.actions'
 5 | 
 6 | export interface InitializeParams {
 7 |   router: Router
 8 | }
 9 | 
10 | export async function initialize({ router }: InitializeParams) {
11 |   const { persistor, store } = await configureStore({ router })
12 | 
13 |   const { localeKey } = store.getState().settings
14 |   store.dispatch(setLocale(localeKey))
15 | 
16 |   return { persistor, store }
17 | }
18 | 


--------------------------------------------------------------------------------
/tools/install-awscli.sh:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env bash
 2 | 
 3 | # Creates CircleCI contexts and sets environment variables
 4 | # Requires CircleCI Local CLI: https://circleci.com/docs/2.0/local-cli/
 5 | 
 6 | set -o errexit
 7 | set -o pipefail
 8 | shopt -s dotglob
 9 | trap "exit" INT
10 | 
11 | THIS_DIR=$(cd $(dirname "${BASH_SOURCE[0]}"); pwd)
12 | 
13 | pushd /tmp >/dev/null
14 | 
15 | curl -fsS "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
16 | unzip -oqq awscliv2.zip
17 | sudo ./aws/install --update
18 | 
19 | popd >/dev/null
20 | 


--------------------------------------------------------------------------------
/data/case-counts/india/IND-Maharashtra***.tsv:
--------------------------------------------------------------------------------
 1 | # Data source: https://api.rootnet.in/covid19-in/stats/daily
 2 | # Data provenance: https://github.com/amodm/api-covid19-in
 3 | # License: Scraped from Ministry of Health and Family Welfare plus other sources, no clear license
 4 | time	cases	deaths	hospitalized	icu	recovered
 5 | 2020-11-10	1723135	45325			
 6 | 2020-12-17	1886807	48434			
 7 | 2020-12-18	1886807	48499			
 8 | 2021-09-10	6497872	138061			
 9 | 2021-09-11	6497872	138061			
10 | 2021-09-12	6497872	138096			
11 | 2021-09-13	6497877	138142			
12 | 


--------------------------------------------------------------------------------
/src/components/NotFound/NotFoundPage.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | import { Container, Col, Row } from 'reactstrap'
 3 | 
 4 | import { useTranslation } from 'react-i18next'
 5 | 
 6 | export function NotFoundPage() {
 7 |   const { t } = useTranslation()
 8 |   return (
 9 |     <Container>
10 |       <Row>
11 |         <Col>
12 |           <h1 className="h1-notfound">{t('Not found')}</h1>
13 |           <h3 className="text-center h3-notfound">{t('This page does not exist')}</h3>
14 |         </Col>
15 |       </Row>
16 |     </Container>
17 |   )
18 | }
19 | 


--------------------------------------------------------------------------------
/src/helpers/numberFormat.ts:
--------------------------------------------------------------------------------
 1 | import { numbro } from '../i18n/i18n'
 2 | 
 3 | export function numberFormatter(humanize: boolean, round: boolean) {
 4 |   return (value: number) =>
 5 |     numbro(value).format({
 6 |       thousandSeparated: true,
 7 |       average: humanize,
 8 |       trimMantissa: true,
 9 |       mantissa: round ? 0 : 2,
10 |     })
11 | }
12 | 
13 | export function percentageFormatter(value: number, mantissa = 2) {
14 |   return numbro(value).format({
15 |     output: 'percent',
16 |     trimMantissa: true,
17 |     mantissa,
18 |   })
19 | }
20 | 


--------------------------------------------------------------------------------
/src/styles/components/SimulationControls.scss:
--------------------------------------------------------------------------------
 1 | @use "sass:map";
 2 | 
 3 | @import '../variables';
 4 | 
 5 | $lg: map.get($grid-breakpoints, 'lg');
 6 | 
 7 | .btn-simulation-controls {
 8 |   margin-left: 3px;
 9 | 
10 |   @media screen and (min-width: $lg) {
11 |     $btn-size: 45px;
12 | 
13 |     width: $btn-size * 1.333;
14 |     height: $btn-size;
15 | 
16 |     svg {
17 |       fill: $gray-600;
18 |     }
19 | 
20 |     &.btn-run {
21 |       width: $btn-size * 2;
22 | 
23 |       svg {
24 |         fill: $gray-100;
25 |       }
26 |     }
27 |   }
28 | }
29 | 


--------------------------------------------------------------------------------
/config/nodemon/serve.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "quiet": true,
 3 |   "legacyWatch": false,
 4 |   "delay": 0.1,
 5 |   "watch": [
 6 |     ".env",
 7 |     "babel.config.js",
 8 |     "infra/lambda-at-edge/modifyOutgoingHeaders.lambda.js",
 9 |     "package.json",
10 |     "src/server",
11 |     "tsconfig.json",
12 |     "yarn.lock"
13 |   ],
14 |   "ext": "js,jsx,ts,tsx,json,flow,css,scss,sass,styl,html,ejs,d,txt,yml,sh",
15 |   "ignore": ["**/*.test.*s", "**/*.test.*sx", "**/__tests__", ".build", "config/jest", "node_modules"],
16 |   "exec": "yarn prod:serve:nowatch || cd ."
17 | }
18 | 


--------------------------------------------------------------------------------
/schemas/DateRange.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: DateRange
 3 | title: DateRange
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - begin
11 |   - end
12 | 
13 | properties:
14 |   begin:
15 |     oneOf:
16 |       - type: string
17 |         format: date
18 |       - type: string
19 |         format: date-time
20 |     formatMaximum:
21 |       $data: '1/end'
22 | 
23 |   end:
24 |     oneOf:
25 |       - type: string
26 |         format: date
27 |       - type: string
28 |         format: date-time
29 | 


--------------------------------------------------------------------------------
/schemas/Shareable.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: Shareable
 3 | title: Shareable
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - schemaVer
11 |   - scenarioData
12 |   - ageDistributionData
13 |   - severityDistributionData
14 | 
15 | properties:
16 |   schemaVer:
17 |     $ref: '_SchemaVer#'
18 | 
19 |   scenarioData:
20 |     $ref: 'ScenarioData#'
21 | 
22 |   ageDistributionData:
23 |     $ref: 'AgeDistributionData#'
24 | 
25 |   severityDistributionData:
26 |     $ref: 'SeverityDistributionData#'
27 | 


--------------------------------------------------------------------------------
/schemas/ScenarioDatum.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: ScenarioDatum
 3 | title: ScenarioDatum
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - population
11 |   - epidemiological
12 |   - simulation
13 |   - mitigation
14 | 
15 | properties:
16 |   population:
17 |     $ref: 'ScenarioDatumPopulation#'
18 | 
19 |   epidemiological:
20 |     $ref: 'ScenarioDatumEpidemiological#'
21 | 
22 |   simulation:
23 |     $ref: 'ScenarioDatumSimulation#'
24 | 
25 |   mitigation:
26 |     $ref: 'ScenarioDatumMitigation#'
27 | 


--------------------------------------------------------------------------------
/src/styles/components/ModalButtonSharing.scss:
--------------------------------------------------------------------------------
 1 | @use "sass:map";
 2 | 
 3 | @import '../variables';
 4 | 
 5 | $lg: map.get($grid-breakpoints, 'lg');
 6 | 
 7 | .url-text-input.form-control {
 8 |   min-height: 45px;
 9 |   font-family: $font-family-monospace;
10 |   background-color: $white;
11 | }
12 | 
13 | .url-copy-button {
14 |   min-width: 120px;
15 |   min-height: 45px;
16 | }
17 | 
18 | .btn-sharing {
19 |   min-width: 100px;
20 |   min-height: 100px;
21 | }
22 | 
23 | .shareable-link-explanation {
24 |   @media screen and (min-width: $lg) {
25 |     width: 75%;
26 |   }
27 | }
28 | 


--------------------------------------------------------------------------------
/src/types/core-js.d.ts:
--------------------------------------------------------------------------------
 1 | declare module 'core-js/es/map'
 2 | declare module 'core-js/es/object/assign'
 3 | declare module 'core-js/es/object/define-properties'
 4 | declare module 'core-js/es/object/define-property'
 5 | declare module 'core-js/es/object/entries'
 6 | declare module 'core-js/es/object/from-entries'
 7 | declare module 'core-js/es/object/keys'
 8 | declare module 'core-js/es/object/values'
 9 | declare module 'core-js/es/set'
10 | declare module 'core-js/es/string/ends-with'
11 | declare module 'core-js/es/string/includes'
12 | declare module 'core-js/es/string/starts-with'
13 | 


--------------------------------------------------------------------------------
/config/next/withMdx.ts:
--------------------------------------------------------------------------------
 1 | import withMDX from '@next/mdx'
 2 | 
 3 | import remarkImages from 'remark-images'
 4 | import remarkMath from 'remark-math'
 5 | import remarkSmartypants from '@silvenon/remark-smartypants'
 6 | import rehypeKatex from 'rehype-katex'
 7 | 
 8 | export default withMDX({
 9 |   extension: /\.mdx?$/,
10 |   options: {
11 |     remarkPlugins: [
12 |       [remarkImages, {}],
13 |       [remarkMath, {}],
14 |       [remarkSmartypants, { quotes: false, backticks: false, ellipses: false, dashes: 'oldschool' }],
15 |     ],
16 |     rehypePlugins: [rehypeKatex],
17 |   },
18 | })
19 | 


--------------------------------------------------------------------------------
/docker/docker-compose.codeclimate.yml:
--------------------------------------------------------------------------------
 1 | version: '3.7'
 2 | 
 3 | services:
 4 |   codeclimate:
 5 |     container_name: codeclimate
 6 |     image: codeclimate/codeclimate:latest
 7 |     command: analyze
 8 |     volumes:
 9 |       - ../:/code
10 |       - /etc/timezone:/etc/timezone:ro
11 |       - /etc/localtime:/etc/localtime:ro
12 |       - /var/run/docker.sock:/var/run/docker.sock
13 |       - /tmp/cc:/tmp/cc
14 |     environment:
15 |       - CODECLIMATE_CODE=${PWD}
16 |       - COLORTERM=truecolor
17 |       - TERM=xterm-truecolor
18 |     restart: 'no'
19 |     init: true
20 |     tty: true
21 | 


--------------------------------------------------------------------------------
/config/next/withIgnore.ts:
--------------------------------------------------------------------------------
 1 | import webpack from 'webpack'
 2 | import type { NextConfig } from 'next'
 3 | 
 4 | import { addWebpackPlugin } from './lib/addWebpackPlugin'
 5 | 
 6 | export default function withIgnore(nextConfig: NextConfig) {
 7 |   return addWebpackPlugin(
 8 |     nextConfig,
 9 |     new webpack.IgnorePlugin({
10 |       checkResource: (resource: string) => {
11 |         return (
12 |           resource.endsWith('awesomplete.css') ||
13 |           resource.includes('core-js/library') ||
14 |           resource.includes('babel-runtime')
15 |         )
16 |       },
17 |     }),
18 |   )
19 | }
20 | 


--------------------------------------------------------------------------------
/src/components/Form/HelpLabel.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import _ from 'lodash'
 4 | 
 5 | import FormHelpButton from './FormHelpButton'
 6 | 
 7 | export interface HelpLabelProps {
 8 |   identifier: string
 9 |   label: string | React.ReactNode
10 |   help?: string | React.ReactNode
11 | }
12 | 
13 | export default function HelpLabel({ identifier, label, help }: HelpLabelProps) {
14 |   return (
15 |     <div className="d-flex align-items-center">
16 |       <span className="my-auto">{label}</span>
17 |       {help && !_.isEmpty(help) && <FormHelpButton help={help} />}
18 |     </div>
19 |   )
20 | }
21 | 


--------------------------------------------------------------------------------
/src/components/Form/__tests__/HelpLabel.test.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | import { render } from '@testing-library/react'
 3 | import HelpLabel from '../HelpLabel'
 4 | 
 5 | describe('HelpLabel', () => {
 6 |   it('displays the label', () => {
 7 |     const { getByText } = render(<HelpLabel identifier="abc" label="def" />)
 8 | 
 9 |     expect(getByText('def')).not.toBeNull()
10 |   })
11 | 
12 |   it('displays a help button', () => {
13 |     const { getByLabelText } = render(<HelpLabel identifier="abc" label="def" help="ghi" />)
14 | 
15 |     expect(getByLabelText('help')).not.toBeNull()
16 |   })
17 | })
18 | 


--------------------------------------------------------------------------------
/.env.vercel:
--------------------------------------------------------------------------------
 1 | FULL_DOMAIN=autodetect
 2 | 
 3 | WEB_PORT_DEV=3000
 4 | WEB_PORT_PROD=null
 5 | WEB_PORT_ANALYZE=8888
 6 | 
 7 | NEXT_TELEMETRY_DISABLED=0
 8 | 
 9 | DEV_ENABLE_TYPE_CHECKS=1
10 | DEV_ENABLE_ESLINT=1
11 | DEV_ENABLE_STYLELINT=1
12 | DEV_ENABLE_REDUX_DEV_TOOLS=1
13 | DEV_ENABLE_REDUX_IMMUTABLE_STATE_INVARIANT=0
14 | DEV_ENABLE_REDUX_LOGGER=0
15 | 
16 | PROD_ENABLE_SOURCE_MAPS=1
17 | PROD_ENABLE_TYPE_CHECKS=0
18 | PROD_ENABLE_ESLINT=0
19 | PROD_ENABLE_STYLELINT=0
20 | PROD_ENABLE_REDUX_DEV_TOOLS=1
21 | PROD_ENABLE_REDUX_IMMUTABLE_STATE_INVARIANT=0
22 | PROD_ENABLE_REDUX_LOGGER=0
23 | 
24 | ANALYZE=0
25 | PROFILE=0
26 | 


--------------------------------------------------------------------------------
/lib/findModuleRoot.js:
--------------------------------------------------------------------------------
 1 | const fs = require('fs-extra')
 2 | const path = require('path')
 3 | 
 4 | /* eslint-disable no-loops/no-loops,no-param-reassign,no-plusplus */
 5 | module.exports = {
 6 |   findModuleRoot(maxDepth = 10) {
 7 |     let moduleRoot = __dirname
 8 |     while (--maxDepth) {
 9 |       moduleRoot = path.resolve(moduleRoot, '..')
10 |       const file = path.join(moduleRoot, 'package.json')
11 |       if (fs.existsSync(file)) {
12 |         const pkg = fs.readJsonSync(file)
13 |         return { moduleRoot, pkg }
14 |       }
15 |     }
16 |     throw new Error('Module root not found')
17 |   },
18 | }
19 | 


--------------------------------------------------------------------------------
/src/components/Buttons/LinkButton.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import { Button, ButtonProps } from 'reactstrap'
 4 | 
 5 | interface LinkButtonProps extends React.PropsWithChildren<ButtonProps> {
 6 |   href?: string
 7 |   target: '_blank' | '_self' | '_parent' | '_top'
 8 | }
 9 | 
10 | const LinkButton = ({ href, target = '_self', type = 'button', children, ...restProps }: LinkButtonProps) => {
11 |   return (
12 |     <a href={href} target={target}>
13 |       <Button type={type} {...restProps}>
14 |         {children}
15 |       </Button>
16 |     </a>
17 |   )
18 | }
19 | 
20 | export default LinkButton
21 | 


--------------------------------------------------------------------------------
/src/styles/_mixins.scss:
--------------------------------------------------------------------------------
 1 | @import './variables';
 2 | 
 3 | @mixin horizontal-scroll-shadow($shadow-color: rgba($black, 0.33), $shadow-width: 33px) {
 4 |   // prettier-ignore
 5 |   background:
 6 |     linear-gradient(90deg, $white 0%, transparent),
 7 |     linear-gradient(-90deg, $white 0%, transparent) 100% 0,
 8 |     linear-gradient(90deg, $shadow-color, transparent),
 9 |     linear-gradient(-90deg, $shadow-color, transparent) 100% 0;
10 |   background-repeat: no-repeat;
11 |   background-attachment: local, local, scroll, scroll;
12 |   background-size: 100px 100%, 100px 100%, $shadow-width 100%, $shadow-width 100%;
13 | }
14 | 


--------------------------------------------------------------------------------
/src/types/preload-webpack-plugin.d.ts:
--------------------------------------------------------------------------------
 1 | declare module 'preload-webpack-plugin' {
 2 |   type AsFunction = (entry: string) => string
 3 | 
 4 |   export interface PreloadWebpackPluginOptions {
 5 |     rel: 'preload'
 6 | 
 7 |     as: 'script' | 'font' | AsFunction
 8 | 
 9 |     include: 'initial' | 'asyncChunks' | 'allChunks' | 'allAssets' | string[]
10 | 
11 |     fileBlacklist: string[] | RegExp[]
12 | 
13 |     excludeHtmlNames: string[]
14 |   }
15 | 
16 |   declare class PreloadWebpackPlugin {
17 |     public constructor(PreloadWebpackPluginOptions: options)
18 |   }
19 | 
20 |   export default PreloadWebpackPlugin
21 | }
22 | 


--------------------------------------------------------------------------------
/src/components/Main/Results/chartHelper.ts:
--------------------------------------------------------------------------------
 1 | import { MutableRefObject } from 'react'
 2 | 
 3 | import { Coordinate } from 'recharts'
 4 | 
 5 | const singleColumnThreshold = 992
 6 | 
 7 | export function calculatePosition(height: number): Coordinate | undefined {
 8 |   if (window.innerWidth < singleColumnThreshold) {
 9 |     return { x: 0, y: height - 20 }
10 |   }
11 |   return undefined
12 | }
13 | 
14 | export function scrollToRef(ref: MutableRefObject<HTMLElement | null>) {
15 |   if (window.innerWidth < singleColumnThreshold) {
16 |     ref.current?.scrollIntoView({
17 |       behavior: 'smooth',
18 |     })
19 |   }
20 | }
21 | 


--------------------------------------------------------------------------------
/src/styles/components/NavigationBar.scss:
--------------------------------------------------------------------------------
 1 | @import '../variables';
 2 | 
 3 | .navbar {
 4 |   min-width: 2em;
 5 |   box-shadow: 2px 2px 5px 5px $gray-400;
 6 | 
 7 |   &.navbar-dark.bg-dark {
 8 |     background-color: $gray-800 !important;
 9 |   }
10 | 
11 |   .navbar-brand {
12 |     padding: 0;
13 |   }
14 | }
15 | 
16 | .navbar-scroll {
17 |   overflow-x: auto;
18 |   white-space: nowrap;
19 |   -webkit-overflow-scrolling: touch;
20 | }
21 | 
22 | .navigation-bar-product-logo {
23 |   width: 35px;
24 |   height: 35px;
25 |   margin-left: 5px;
26 | }
27 | 
28 | .navigation-bar-company-logo {
29 |   width: 26px;
30 |   height: 26px;
31 | }
32 | 


--------------------------------------------------------------------------------
/src/state/settings/settings.sagas.ts:
--------------------------------------------------------------------------------
 1 | import { takeEvery, call, put } from 'typed-redux-saga'
 2 | 
 3 | import { Action } from 'typescript-fsa'
 4 | 
 5 | import i18n, { changeLocale, DEFAULT_LOCALE_KEY, LocaleKey } from '../../i18n/i18n'
 6 | import { setLocale } from './settings.actions'
 7 | 
 8 | export function* onSetLocale({ payload }: Action<LocaleKey>) {
 9 |   const localeKey = payload
10 | 
11 |   const localeChangedSuccessfully = yield* call(changeLocale, i18n, localeKey)
12 |   if (!localeChangedSuccessfully) {
13 |     yield* put(setLocale(DEFAULT_LOCALE_KEY))
14 |   }
15 | }
16 | 
17 | export default [takeEvery(setLocale, onSetLocale)]
18 | 


--------------------------------------------------------------------------------
/public/manifest.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "short_name": "COVID-19 Scenarios",
 3 |   "name": "COVID-19 Scenarios",
 4 |   "description": "Models of COVID-19 outbreak trajectories and hospital demand",
 5 |   "theme_color": "#343a40",
 6 |   "background_color": "#000007",
 7 |   "start_url": "/?source=pwa",
 8 |   "display": "standalone",
 9 |   "scope": "/",
10 |   "icons": [
11 |     {
12 |       "src": "/icons/android-chrome-192x192.png",
13 |       "sizes": "192x192",
14 |       "type": "image/png"
15 |     },
16 |     {
17 |       "src": "/icons/android-chrome-512x512.png",
18 |       "sizes": "512x512",
19 |       "type": "image/png"
20 |     }
21 |   ]
22 | }
23 | 


--------------------------------------------------------------------------------
/src/components/Link/Link.tsx:
--------------------------------------------------------------------------------
 1 | import React, { HTMLAttributes, PropsWithChildren } from 'react'
 2 | 
 3 | import NextLink, { LinkProps as NextLinkProps } from 'next/link'
 4 | 
 5 | export interface LinkProps extends PropsWithChildren<NextLinkProps & HTMLAttributes<HTMLAnchorElement>> {
 6 |   className?: string
 7 | }
 8 | 
 9 | export function Link({ className, children, href, ...restProps }: LinkProps) {
10 |   return (
11 |     <NextLink href={href} passHref={false}>
12 |       {/* eslint-disable-next-line jsx-a11y/anchor-is-valid */}
13 |       <a className={className}>{children}</a>
14 |     </NextLink>
15 |   )
16 | }
17 | 
18 | export default Link
19 | 


--------------------------------------------------------------------------------
/src/algorithms/utils/sample.ts:
--------------------------------------------------------------------------------
 1 | import { NumericRangeNonNegative } from '../types/Param.types'
 2 | 
 3 | // TODO(nnoll): Generalize to allow for sampling multiple uncertainty ranges
 4 | export function sampleUniform({ begin, end }: NumericRangeNonNegative, npoints: number): number[] {
 5 |   const sample: number[] = []
 6 |   const delta = (end - begin) / npoints
 7 |   let val = begin
 8 |   while (sample.length < npoints) {
 9 |     sample.push(val)
10 |     val += delta
11 |   }
12 |   return sample
13 | }
14 | 
15 | export function sampleRandom({ begin, end }: NumericRangeNonNegative): number {
16 |   return (end - begin) * Math.random() + begin
17 | }
18 | 


--------------------------------------------------------------------------------
/src/components/Layout/NavigationLink.tsx:
--------------------------------------------------------------------------------
 1 | import React, { HTMLProps, PropsWithChildren } from 'react'
 2 | 
 3 | import classNames from 'classnames'
 4 | 
 5 | import { Link } from 'src/components/Link/Link'
 6 | 
 7 | export interface NavigationLinkProps extends PropsWithChildren<HTMLProps<HTMLDataListElement>> {
 8 |   active?: boolean
 9 |   url: string
10 | }
11 | 
12 | export default function NavigationLink({ active, url, children }: NavigationLinkProps) {
13 |   return (
14 |     <li className={classNames('nav-item', active && 'active')}>
15 |       <Link className="nav-link" href={url}>
16 |         {children}
17 |       </Link>
18 |     </li>
19 |   )
20 | }
21 | 


--------------------------------------------------------------------------------
/src/components/Faq/Faq.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import { useTranslation } from 'react-i18next'
 4 | import { Col, Container, Row } from 'reactstrap'
 5 | 
 6 | import FaqTableOfContents from './FaqTableOfContents'
 7 | 
 8 | import FaqContent from './FaqContent.mdx'
 9 | 
10 | export function Faq() {
11 |   const { t } = useTranslation()
12 | 
13 |   return (
14 |     <Container>
15 |       <Row>
16 |         <Col>
17 |           <h1 className="h1-default">{t('Frequently asked questions')}</h1>
18 |           <FaqTableOfContents />
19 |           <hr />
20 |           <FaqContent />
21 |         </Col>
22 |       </Row>
23 |     </Container>
24 |   )
25 | }
26 | 


--------------------------------------------------------------------------------
/src/state/error/error.reducer.ts:
--------------------------------------------------------------------------------
 1 | import { Action } from 'redux'
 2 | import { isType } from 'typescript-fsa'
 3 | 
 4 | import { errorAdd, errorDismiss } from './error.actions'
 5 | 
 6 | export interface ErrorState {
 7 |   error: string | null
 8 | }
 9 | 
10 | export const errorDefaultState: ErrorState = {
11 |   error: null,
12 | }
13 | 
14 | export function errorReducer(state: ErrorState = errorDefaultState, action: Action) {
15 |   if (isType(action, errorAdd)) {
16 |     return { ...state, error: action.payload.error.message }
17 |   }
18 | 
19 |   if (isType(action, errorDismiss)) {
20 |     return { ...state, error: null }
21 |   }
22 | 
23 |   return state
24 | }
25 | 


--------------------------------------------------------------------------------
/src/components/Loading/Loading.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import { Container, Row, Col } from 'reactstrap'
 4 | 
 5 | import { useTranslation } from 'react-i18next'
 6 | 
 7 | function Loading() {
 8 |   const { t } = useTranslation()
 9 |   return (
10 |     <Container>
11 |       <Row>
12 |         <Col>
13 |           <div className="loading-page d-flex justify-content-center">
14 |             <div className="spinner-border" role="status">
15 |               <span className="sr-only">{t('Loading...')}</span>
16 |             </div>
17 |           </div>
18 |         </Col>
19 |       </Row>
20 |     </Container>
21 |   )
22 | }
23 | 
24 | export default Loading
25 | 


--------------------------------------------------------------------------------
/data/scripts/default_schema_values.py:
--------------------------------------------------------------------------------
 1 | # ------------------------------------------------------------------------
 2 | # Globals
 3 | 
 4 | DEFAULTS = {
 5 |         "PopulationData" : {
 6 |           "seroprevalence": 0.0,
 7 |         },
 8 |         "EpidemiologicalData" : {
 9 |             "latencyTime" : 3.0,
10 |             "infectiousPeriod" : 3.0,
11 |             "lengthHospitalStay": 7.0,
12 |             "lengthICUStay": 14.0,
13 |             "seasonalForcing": 0.0,
14 |             "peakMonth": 0,
15 |             "overflowSeverity": 2.0,
16 |             "r0": 3.0,
17 |          },
18 |         "ContainmentData": {
19 |             "numberPoints": 15.0
20 |          }
21 | }
22 | 


--------------------------------------------------------------------------------
/data/case-counts/ecdc/Saint Barthelemy.tsv:
--------------------------------------------------------------------------------
1 | # Data source: https://www.ecdc.europa.eu/sites/default/files/documents/COVID-19-geographic-disbtribution-worldwide-<DATE>-xlsx
2 | # Data provenance: European Centre for Disease Prevention and Control
3 | # License: The downloadable data file is updated daily and contains the latest available public data on COVID-19. Public-use data files allows users to manipulate the data in a format appropriate for their analyses. Users of ECDC public-use data files must comply with data use restrictions to ensure that the information will be used solely for statistical analysis or reporting purposes.
4 | time	cases	deaths	hospitalized	icu	recovered
5 | 2020-04-02	6	0			
6 | 


--------------------------------------------------------------------------------
/data/scripts/validateAge.py:
--------------------------------------------------------------------------------
 1 | import os, json, yaml
 2 | 
 3 | from jsonschema import validate, FormatChecker
 4 | 
 5 | PATH_UN_AGES   = os.path.join("../", "../src/assets/data/country_age_distribution.json")
 6 | 
 7 | with open(os.path.join('../../schemas/CountryAgeDistribution.yml'), "r") as f:
 8 |     schema = yaml.load(f, Loader=yaml.FullLoader)
 9 | 
10 | with open(PATH_UN_AGES, 'r') as f:
11 |     data = json.load(f)
12 |     
13 | validate(data, schema, format_checker=FormatChecker())
14 | 
15 | data = sorted(data, key=lambda x: x['country'])
16 | 
17 | with open(PATH_UN_AGES, 'w') as f:
18 |     json.dump(data, f, indent=0)
19 | 
20 | print(f'Validated age distribution data with len {len(data)}')
21 | 


--------------------------------------------------------------------------------
/src/components/Main/Scenario/SeverityCardInfo.mdx:
--------------------------------------------------------------------------------
1 | #### Summary of demographics and age-dependent parameters.
2 | 
3 | The second column shows how many people fall into each age group. The following columns summarize COVID19 severity
4 | informed by epidemiological and clinical observations from China, Spain, Switzerland, and Italy. The column "Confirmed"
5 | reflects our assumption on what fraction of infections are reflected in the statistics, the following columns contain
6 | the assumption on what fraction of the previous category deteriorates to the next. Most fields are editable and can be
7 | adjusted to different assumptions. The last column can be used to specify age-group-specific isolation measures.
8 | 


--------------------------------------------------------------------------------
/src/state/algorithm/algorithm.actions.ts:
--------------------------------------------------------------------------------
 1 | import actionCreatorFactory from 'typescript-fsa'
 2 | 
 3 | import type { AlgorithmResult } from '../../algorithms/types/Result.types'
 4 | import type { RunParams } from '../../algorithms/run'
 5 | 
 6 | const action = actionCreatorFactory('ALGORITHM')
 7 | 
 8 | export const algorithmRunTrigger = action('RUN_TRIGGER')
 9 | 
10 | export interface AlgorithmRunParams {
11 |   params: RunParams
12 | }
13 | 
14 | export interface AlgorithmRunResults {
15 |   result: AlgorithmResult
16 | }
17 | 
18 | export interface AlgorithmRunError {
19 |   error: Error
20 | }
21 | 
22 | export const algorithmRunAsync = action.async<void, AlgorithmRunResults, AlgorithmRunError>('RUN')
23 | 


--------------------------------------------------------------------------------
/config/next/lib/addWebpackLoader.ts:
--------------------------------------------------------------------------------
 1 | import type { NextConfig, NextWebpackOptions } from 'next'
 2 | 
 3 | import type { WebpackOptions, RuleSetRule } from 'webpack/declarations/WebpackOptions'
 4 | 
 5 | import { addWebpackConfig } from './addWebpackConfig'
 6 | 
 7 | export type GetLoaderFunction = (webpackConfig: WebpackOptions, options: NextWebpackOptions) => RuleSetRule
 8 | 
 9 | export function addWebpackLoader(nextConfig: NextConfig, getLoader: GetLoaderFunction) {
10 |   return addWebpackConfig(nextConfig, (nextConfig, webpackConfig, options) => {
11 |     const loader = getLoader(webpackConfig, options)
12 |     webpackConfig?.module?.rules?.push(loader)
13 |     return webpackConfig
14 |   })
15 | }
16 | 


--------------------------------------------------------------------------------
/tools/trigger-data-update.sh:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env bash
 2 | 
 3 | set -o errexit
 4 | set -o nounset
 5 | set -o pipefail
 6 | shopt -s dotglob
 7 | trap "exit" INT
 8 | 
 9 | THIS_DIR=$(
10 |   cd $(dirname "${BASH_SOURCE[0]}")
11 |   pwd
12 | )
13 | 
14 | # Put your GITHUB_TOKEN into .env file
15 | [ -f "${THIS_DIR}/../.env" ] && source "${THIS_DIR}/../.env"
16 | 
17 | # or set an environment variable (not recommended)
18 | GITHUB_TOKEN=${GITHUB_TOKEN:?GITHUB_TOKEN is required}
19 | 
20 | 
21 | curl -i https://api.github.com/repos/neherlab/covid19_scenarios/dispatches \
22 |   -H "Accept: application/vnd.github.v3+json" \
23 |   -H "Authorization: token ${GITHUB_TOKEN}" \
24 |   -d '{ "event_type": "update-case-counts-data" }' \
25 | 


--------------------------------------------------------------------------------
/schemas/SeverityDistributionDatum.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: SeverityDistributionDatum
 3 | title: SeverityDistributionDatum
 4 | 
 5 | additionalProperties: false
 6 | 
 7 | type: object
 8 | 
 9 | required:
10 |   - ageGroup
11 |   - isolated
12 |   - palliative
13 |   - confirmed
14 |   - severe
15 |   - critical
16 |   - fatal
17 | 
18 | properties:
19 |   ageGroup:
20 |     $ref: 'AgeGroup#'
21 | 
22 |   isolated:
23 |     $ref: 'Percentage#'
24 | 
25 |   palliative:
26 |     $ref: 'Percentage#'
27 | 
28 |   confirmed:
29 |     $ref: 'Percentage#'
30 | 
31 |   severe:
32 |     $ref: 'Percentage#'
33 | 
34 |   critical:
35 |     $ref: 'Percentage#'
36 | 
37 |   fatal:
38 |     $ref: 'Percentage#'
39 | 


--------------------------------------------------------------------------------
/lib/getenv.js:
--------------------------------------------------------------------------------
 1 | const EnvVarError = require('./EnvVarError')
 2 | 
 3 | function getenv(key, defaultValue) {
 4 |   const value = process.env[key]
 5 |   if (!value) {
 6 |     if (typeof defaultValue !== 'undefined') {
 7 |       return defaultValue
 8 |     }
 9 | 
10 |     throw new EnvVarError(key, value)
11 |   }
12 |   return value
13 | }
14 | 
15 | function getbool(key, defaultValue) {
16 |   const value = process.env[key]
17 |   if (!value) {
18 |     if (typeof defaultValue !== 'undefined') {
19 |       return defaultValue
20 |     }
21 | 
22 |     throw new EnvVarError(key, value)
23 |   }
24 | 
25 |   return value === '1' || value === 'true' || value === 'yes'
26 | }
27 | 
28 | module.exports = {
29 |   getenv,
30 |   getbool,
31 | }
32 | 


--------------------------------------------------------------------------------
/config/next/lib/addWebpackConfig.ts:
--------------------------------------------------------------------------------
 1 | import type { NextWebpackOptions, NextConfig } from 'next'
 2 | import type { WebpackOptions } from 'webpack/declarations/WebpackOptions'
 3 | 
 4 | import { CustomWebpackConfig } from './CustomWebpackConfig'
 5 | 
 6 | export function addWebpackConfig(nextConfig: NextConfig, customWebpackConfig: CustomWebpackConfig) {
 7 |   const webpack = (webpackConfig: WebpackOptions, options: NextWebpackOptions) => {
 8 |     const newConfig = customWebpackConfig(nextConfig, webpackConfig, options)
 9 | 
10 |     if (typeof nextConfig.webpack === 'function') {
11 |       return nextConfig.webpack(newConfig, options)
12 |     }
13 | 
14 |     return newConfig
15 |   }
16 | 
17 |   return { ...nextConfig, webpack }
18 | }
19 | 


--------------------------------------------------------------------------------
/config/nodemon/stylelint.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "quiet": true,
 3 |   "legacyWatch": false,
 4 |   "delay": 0.1,
 5 |   "watch": [
 6 |     "../.env",
 7 |     ".browserslistrc",
 8 |     ".editorconfig",
 9 |     ".env",
10 |     ".prettierignore",
11 |     ".prettierrc",
12 |     "config",
13 |     "jest.config.js",
14 |     "package.json",
15 |     "postcss.config.js",
16 |     "src",
17 |     "static",
18 |     "stylelint.config.js",
19 |     "yarn.lock"
20 |   ],
21 |   "ext": "js,jsx,ts,tsx,json,flow,css,scss,sass,styl,html,ejs,d,txt,yml,sh",
22 |   "ignore": ["**/*.test.*s", "**/*.test.*sx", "**/__tests__", ".build", "config/jest", "node_modules"],
23 |   "exec": "yarn clear && yarn stylelint && echo '\u2714 OK' || echo '\u274C FAILED' || cd ."
24 | }
25 | 


--------------------------------------------------------------------------------
/config/nodemon/stylelint.fix.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "quiet": true,
 3 |   "legacyWatch": false,
 4 |   "delay": 0.1,
 5 |   "watch": [
 6 |     "../.env",
 7 |     ".browserslistrc",
 8 |     ".editorconfig",
 9 |     ".env",
10 |     ".prettierignore",
11 |     ".prettierrc",
12 |     "config",
13 |     "jest.config.js",
14 |     "package.json",
15 |     "postcss.config.js",
16 |     "src",
17 |     "static",
18 |     "stylelint.config.js",
19 |     "yarn.lock"
20 |   ],
21 |   "ext": "js,jsx,ts,tsx,json,flow,css,scss,sass,styl,html,ejs,d,txt,yml,sh",
22 |   "ignore": ["**/*.test.*s", "**/*.test.*sx", "**/__tests__", ".build", "config/jest", "node_modules"],
23 |   "exec": "yarn clear && yarn stylelint:fix && echo '\u2714 OK' || echo '\u274C FAILED'|| cd ."
24 | }
25 | 


--------------------------------------------------------------------------------
/data/case-counts/china/CHN-Qinghai.tsv:
--------------------------------------------------------------------------------
 1 | # Data source: https://github.com/BlankerL/DXY-COVID-19-Data/raw/master/csv/DXYOverall.csv
 2 | # Data provenance: https://github.com/BlankerL/DXY-COVID-19-Data
 3 | # License: MIT
 4 | time	cases	deaths	hospitalized	icu	recovered
 5 | 2020-01-24	0	0			0
 6 | 2020-01-25	1	0			0
 7 | 2020-01-27	6	0			0
 8 | 2020-01-30	6	0			0
 9 | 2020-01-31	8	0			0
10 | 2020-02-01	9	0			0
11 | 2020-02-02	11	0			0
12 | 2020-02-03	13	0			0
13 | 2020-02-04	15	0			0
14 | 2020-02-05	17	0			3
15 | 2020-02-06	18	0			3
16 | 2020-02-11	18	0			5
17 | 2020-02-12	18	0			9
18 | 2020-02-13	18	0			11
19 | 2020-02-15	18	0			13
20 | 2020-02-18	18	0			15
21 | 2020-02-19	18	0			16
22 | 2020-02-21	18	0			18
23 | 2020-02-23	18	0			18
24 | 


--------------------------------------------------------------------------------
/lib/EnvVarError.js:
--------------------------------------------------------------------------------
 1 | class EnvVarError extends TypeError {
 2 |   constructor(key, value) {
 3 |     super(`
 4 |       When reading an environement variable "${key}" (as \`process.env.${key}\`):
 5 |       it was expected to find a valid string, but found \`${value}\`.
 6 | 
 7 |       Have you followed the instructions in Developer's guide?
 8 | 
 9 |       There might have been additions to the list of environement variables required.
10 |       Verify that your \`.env\` file has all the variables present in \`.env.example\`:
11 | 
12 |         diff --color .env.example .env
13 | 
14 |       In simple cases you might just copy the example:
15 | 
16 |         cp .env.example .env
17 | 
18 |       `)
19 |   }
20 | }
21 | 
22 | module.exports = EnvVarError
23 | 


--------------------------------------------------------------------------------
/src/styles/components/FormHelpButton.scss:
--------------------------------------------------------------------------------
 1 | @import '../variables';
 2 | 
 3 | $btn-radius: 16px;
 4 | 
 5 | .help-button {
 6 |   display: flex;
 7 |   width: $btn-radius;
 8 |   height: $btn-radius;
 9 |   padding: 0;
10 |   background-color: $gray-200;
11 |   border: 0;
12 |   border-radius: $btn-radius / 2;
13 |   align-items: center;
14 |   justify-content: center;
15 | }
16 | 
17 | .help-button-icon {
18 |   font-family: $font-family-monospace;
19 |   font-size: $btn-radius * 0.85;
20 |   font-weight: bold;
21 |   color: $gray-600;
22 |   text-align: center;
23 |   vertical-align: middle;
24 | }
25 | 
26 | .card.card-help {
27 |   border-radius: 3px;
28 | 
29 |   .card-body.card-body-help {
30 |     p {
31 |       color: $body-color;
32 |     }
33 |   }
34 | }
35 | 


--------------------------------------------------------------------------------
/src/helpers/errorPrototypeTojson.ts:
--------------------------------------------------------------------------------
 1 | /* eslint-disable no-inner-declarations,cflint/no-this-assignment,@typescript-eslint/ban-ts-comment,no-extend-native */
 2 | // @ts-ignore
 3 | import { appendDash } from './appendDash'
 4 | 
 5 | // @ts-ignore
 6 | if (!Error.prototype.toJSON) {
 7 |   function toJSON(this: Error) {
 8 |     const { message, name, stack } = this
 9 |     const stackPretty = stack?.split('\n').map(appendDash)
10 |     return { message, name, stack: stackPretty }
11 |   }
12 |   if (Object.defineProperty) {
13 |     Object.defineProperty(Error.prototype, 'toJSON', {
14 |       value: toJSON,
15 |       configurable: true,
16 |       writable: true,
17 |     })
18 |   } else {
19 |     // @ts-ignore
20 |     Error.prototype.toJSON = toJSON
21 |   }
22 | }
23 | 


--------------------------------------------------------------------------------
/docker/python-pip/Dockerfile:
--------------------------------------------------------------------------------
 1 | FROM ubuntu:bionic-20191029
 2 | 
 3 | ENV DEBIAN_FRONTEND=noninteractive
 4 | ENV LC_ALL=C.UTF-8
 5 | ENV LANG=C.UTF-8
 6 | ENV PYTHONDONTWRITEBYTECODE=1
 7 | 
 8 | RUN apt-get update -qq \
 9 | && apt-get install --no-install-recommends --yes --force-yes -qq \
10 |   curl \
11 |   git \
12 |   libffi-dev \
13 |   make \
14 |   python3-pip \
15 |   python3-setuptools \
16 |   python3-wheel \
17 |   python3.8 \
18 |   python3.8-dev \
19 | > /dev/null
20 | 
21 | RUN rm -rf /usr/bin/python3
22 | RUN ln -s /usr/bin/python3.8 /usr/bin/python3
23 | 
24 | # TODO: Replace this with a proper package manager
25 | RUN pip3 install \
26 | ipython \
27 | jsonschema \
28 | matplotlib \
29 | numpy \
30 | pyyaml \
31 | requests \
32 | schemapi \
33 | scipy \
34 | xlrd
35 | 


--------------------------------------------------------------------------------
/src/state/util/fsaImmerReducer.ts:
--------------------------------------------------------------------------------
 1 | import type { DeepWritable } from 'ts-essentials'
 2 | 
 3 | import produce, { Draft } from 'immer'
 4 | import { ActionCreator } from 'typescript-fsa'
 5 | import { ReducerBuilder } from 'typescript-fsa-reducers'
 6 | 
 7 | // https://github.com/dphilipson/typescript-fsa-reducers/issues/30
 8 | export default function immerCase<StateType, PayloadType>(
 9 |   actionCreator: ActionCreator<PayloadType>,
10 |   handler: (draft: Draft<StateType>, payload: DeepWritable<PayloadType>) => void,
11 | ): (reducer: ReducerBuilder<StateType>) => ReducerBuilder<StateType> {
12 |   return (reducer) =>
13 |     reducer.case(actionCreator, (state, payload) =>
14 |       produce(state, (draft) => handler(draft, payload as DeepWritable<PayloadType>)),
15 |     )
16 | }
17 | 


--------------------------------------------------------------------------------
/src/styles/components/CaseCountsUploader.scss:
--------------------------------------------------------------------------------
 1 | @import '../variables';
 2 | 
 3 | .scenario-loader-uploader-container {
 4 |   display: flex;
 5 |   width: 100%;
 6 |   flex-direction: column;
 7 | }
 8 | 
 9 | .case-counts-uploader-error-list {
10 |   max-height: 50vh;
11 |   overflow: scroll;
12 |   flex: 1;
13 | }
14 | 
15 | .case-counts-uploader-error-list-item {
16 |   margin: 0.25em 0;
17 |   overflow-wrap: anywhere;
18 |   flex: 1;
19 | }
20 | 
21 | $upload-zone-fg: $gray-500;
22 | $upload-zone-bg: $gray-100;
23 | 
24 | .upload-zone {
25 |   cursor: pointer;
26 |   background-color: $upload-zone-bg;
27 |   border: 5px $upload-zone-fg dashed;
28 | 
29 |   &.upload-zone-active {
30 |     border-style: dotted;
31 |   }
32 | }
33 | 
34 | .upload-icon {
35 |   fill: $upload-zone-fg;
36 | }
37 | 


--------------------------------------------------------------------------------
/src/components/Main/ScenarioLoader/ScenarioLoaderListItem.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import { NavLink } from 'reactstrap'
 4 | 
 5 | import type { ScenarioOption } from './ScenarioOption'
 6 | 
 7 | export interface ScenarioLoaderListItemProps {
 8 |   option: ScenarioOption
 9 |   onItemClick: (id: string) => void
10 | }
11 | 
12 | export function ScenarioLoaderListItem({ option, onItemClick }: ScenarioLoaderListItemProps) {
13 |   return (
14 |     <div className="scenario-loader-list-item">
15 |       <NavLink
16 |         data-testid="PresetLoaderDialogRowLink"
17 |         onClick={(event) => {
18 |           event.preventDefault()
19 |           onItemClick(option.value)
20 |         }}
21 |       >
22 |         {option.label}
23 |       </NavLink>
24 |     </div>
25 |   )
26 | }
27 | 


--------------------------------------------------------------------------------
/src/helpers/saveTextFile.ts:
--------------------------------------------------------------------------------
 1 | import { saveAs } from 'file-saver'
 2 | 
 3 | export class ExportErrorBlobApiNotSupported extends Error {
 4 |   constructor() {
 5 |     super('Error: when exporting: `Blob()` API is not supported by this browser')
 6 |   }
 7 | }
 8 | 
 9 | export function checkBlobSupport() {
10 |   try {
11 |     return !!new Blob()
12 |   } catch {
13 |     throw new ExportErrorBlobApiNotSupported()
14 |   }
15 | }
16 | 
17 | export interface SaveFileOptions {
18 |   mimeType?: string
19 | }
20 | 
21 | export function saveTextFile(content: string, filename: string, type: string) {
22 |   const blob = new Blob([content], { type })
23 |   saveBlobFile(blob, filename)
24 | }
25 | 
26 | export function saveBlobFile(content: Blob, filename: string) {
27 |   saveAs(content, filename)
28 | }
29 | 


--------------------------------------------------------------------------------
/src/types/jest.d.ts:
--------------------------------------------------------------------------------
 1 | // This file provides type information patches for jest testing environment
 2 | // because tsc and IDEs cannot deduce types from jest config file alone.
 3 | // Order of imports is important!
 4 | 
 5 | import '@testing-library/jest-dom/extend-expect'
 6 | 
 7 | import 'jest-axe'
 8 | 
 9 | import 'jest-extended/types'
10 | 
11 | import 'jest-styled-components'
12 | 
13 | import 'jest-chain'
14 | 
15 | declare global {
16 |   namespace jest {
17 |     interface Matchers<R> {
18 |       // After toBeTruthy() we are certain that the matched value is not null.
19 |       // Modify the return type accordingly.
20 |       toBeTruthy(): NonNullable<R>
21 |     }
22 | 
23 |     interface ChainedMatchers<R> {
24 |       toBeCloseToArraySnapshot(values: number[]): R
25 |     }
26 |   }
27 | }
28 | 


--------------------------------------------------------------------------------
/data_update.sh:
--------------------------------------------------------------------------------
 1 | echo "update data and bump version from $1 to $2"
 2 | 
 3 | git checkout staging
 4 | git pull origin staging
 5 | 
 6 | cd data
 7 | 
 8 | python generate_data.py --fetch
 9 | 
10 | git add case-counts/*tsv
11 | git commit -m "update case count tsv files"
12 | echo "updated and committed tsv files"
13 | 
14 | python generate_data.py --output-cases ../src/assets/data/caseCounts.json
15 | cd ..
16 | git add src/assets/data/caseCounts.json
17 | git commit -m "update case count json"
18 | echo "updated and committed json file"
19 | 
20 | sed -i "s/$1/$2/" package.json
21 | 
22 | git add package.json
23 | git commit -m "version bump to $2"
24 | echo "bumped version to $2"
25 | 
26 | git tag $2
27 | 
28 | git push origin staging
29 | git push origin $2
30 | 
31 | echo "tagged and pushed to staging"
32 | 


--------------------------------------------------------------------------------
/config/nodemon/lint.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "quiet": true,
 3 |   "legacyWatch": false,
 4 |   "delay": 0.1,
 5 |   "watch": [
 6 |     "../.env",
 7 |     ".browserslistrc",
 8 |     ".editorconfig",
 9 |     ".env",
10 |     ".eslintignore",
11 |     ".eslintrc.js",
12 |     ".prettierignore",
13 |     ".prettierrc",
14 |     "babel.config.js",
15 |     "config",
16 |     "cypress",
17 |     "jest.config.js",
18 |     "package.json",
19 |     "src",
20 |     "tsconfig.json",
21 |     "webpack.config.js",
22 |     "yarn.lock"
23 |   ],
24 |   "ext": "js,jsx,ts,tsx,json,flow,css,scss,sass,styl,html,ejs,d,txt,yml,sh",
25 |   "ignore": ["**/*.test.*s", "**/*.test.*sx", "**/__tests__", ".build", "config/jest", "node_modules"],
26 |   "exec": "yarn clear && yarn lint && echo '\u2714 OK' || echo '\u274C FAILED' || cd ."
27 | }
28 | 


--------------------------------------------------------------------------------
/data/scripts/seasonal_R0_explainer.py:
--------------------------------------------------------------------------------
 1 | import matplotlib.pyplot as plt
 2 | import numpy as np
 3 | 
 4 | fig = plt.figure(figsize=(12,6))
 5 | fs = 16
 6 | 
 7 | time = np.arange(12)+0.5 - 3
 8 | 
 9 | R0 = 1.8
10 | eps = 0.4
11 | peak = 0
12 | 
13 | plt.plot(time, R0*(1+eps*np.cos(2*np.pi*(time-peak)/12)), lw=4)
14 | 
15 | plt.plot(time, R0*np.ones_like(time), lw=3, c='#AAAAAA')
16 | plt.plot([0,0], [0,R0*(1+eps)+0.1], lw=3, c='#AAAAAA')
17 | plt.text(time[0], R0*0.9, "Average R0", fontsize=fs)
18 | plt.text(peak+0.1, R0*(1+eps)+0.1, "Peak transmission", fontsize=fs)
19 | plt.ylim([0.0, R0*(1.2+eps)])
20 | plt.ylabel("Seasonal R0", fontsize=fs)
21 | plt.xticks([time[i] for i in [0,3,6,9]], ['Oct', 'Jan', 'Apr', 'Jul'])
22 | plt.tick_params(labelsize=fs)
23 | plt.savefig('src/assets/img/seasonal_illustration.svg')
24 | 


--------------------------------------------------------------------------------
/config/nodemon/lint.fix.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "quiet": true,
 3 |   "legacyWatch": false,
 4 |   "delay": 0.1,
 5 |   "watch": [
 6 |     "../.env",
 7 |     ".browserslistrc",
 8 |     ".editorconfig",
 9 |     ".env",
10 |     ".eslintignore",
11 |     ".eslintrc.js",
12 |     ".prettierignore",
13 |     ".prettierrc",
14 |     "babel.config.js",
15 |     "config",
16 |     "cypress",
17 |     "jest.config.js",
18 |     "package.json",
19 |     "src",
20 |     "tsconfig.json",
21 |     "webpack.config.js",
22 |     "yarn.lock"
23 |   ],
24 |   "ext": "js,jsx,ts,tsx,json,flow,css,scss,sass,styl,html,ejs,d,txt,yml,sh",
25 |   "ignore": ["**/*.test.*s", "**/*.test.*sx", "**/__tests__", ".build", "config/jest", "node_modules"],
26 |   "exec": "yarn clear && yarn lint:fix && echo '\u2714 OK' || echo '\u274C FAILED' || cd ."
27 | }
28 | 


--------------------------------------------------------------------------------
/src/styles/components/ResponsiveTooltipContent.scss:
--------------------------------------------------------------------------------
 1 | @import '../variables';
 2 | 
 3 | .responsive-tooltip-content-base {
 4 |   z-index: 999;
 5 |   padding: 0.25rem;
 6 |   background-color: $white;
 7 |   border: 1px solid rgba(0, 0, 0, 0.5);
 8 | }
 9 | 
10 | .responsive-tooltip-content {
11 |   display: flex;
12 |   flex-direction: column;
13 | }
14 | 
15 | .responsive-tooltip-content-item {
16 |   display: flex;
17 |   padding: 0.25rem 0.6rem;
18 |   flex-direction: row;
19 |   justify-content: space-between;
20 |   align-items: center;
21 | }
22 | 
23 | .responsive-tooltip-content-placeholder {
24 |   min-width: 1rem;
25 | }
26 | 
27 | @media screen and (max-width: 992px) {
28 |   .responsive-tooltip-content {
29 |     display: grid;
30 |     grid-template: 1fr / 1fr 1fr;
31 |     max-width: 90vw;
32 |   }
33 | }
34 | 


--------------------------------------------------------------------------------
/config/nodemon/dev.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "quiet": true,
 3 |   "legacyWatch": false,
 4 |   "delay": 0.1,
 5 |   "watch": [
 6 |     "../.env",
 7 |     ".browserslistrc",
 8 |     ".editorconfig",
 9 |     ".env",
10 |     ".eslintignore",
11 |     ".eslintrc.js",
12 |     ".prettierignore",
13 |     ".prettierrc",
14 |     "babel.config.js",
15 |     "config",
16 |     "next.config.js",
17 |     "package.json",
18 |     "postcss.config.js",
19 |     "schemas",
20 |     "stylelint.config.js",
21 |     "tsconfig.json",
22 |     "webpack.config.js",
23 |     "yarn.lock"
24 |   ],
25 |   "ext": "js,jsx,ts,tsx,json,flow,css,scss,sass,styl,html,ejs,d,txt,yml,sh",
26 |   "ignore": ["**/*.test.*s", "**/*.test.*sx", "**/__tests__", ".build", "config/jest", "node_modules"],
27 |   "exec": "run-s -c clear dev:clean dev:start || cd ."
28 | }
29 | 


--------------------------------------------------------------------------------
/config/next/lib/addWebpackPlugin.ts:
--------------------------------------------------------------------------------
 1 | import type { NextWebpackOptions, NextConfig } from 'next'
 2 | import type { WebpackOptions, WebpackPluginFunction, WebpackPluginInstance } from 'webpack/declarations/WebpackOptions'
 3 | 
 4 | import { addWebpackConfig } from './addWebpackConfig'
 5 | 
 6 | export function addWebpackPlugin(nextConfig: NextConfig, plugin: WebpackPluginInstance | WebpackPluginFunction) {
 7 |   return addWebpackConfig(
 8 |     nextConfig,
 9 |     (nextConfig: NextConfig, webpackConfig: WebpackOptions, { isServer }: NextWebpackOptions) => {
10 |       if (!isServer) {
11 |         if (webpackConfig?.plugins) {
12 |           webpackConfig.plugins.push(plugin)
13 |         } else {
14 |           return { plugins: [plugin] }
15 |         }
16 |       }
17 |       return webpackConfig
18 |     },
19 |   )
20 | }
21 | 


--------------------------------------------------------------------------------
/src/components/Main/ScenarioLoader/ScenarioLoaderCard.tsx:
--------------------------------------------------------------------------------
 1 | import React, { ReactNode } from 'react'
 2 | 
 3 | import c from 'classnames'
 4 | import type { CardProps } from 'reactstrap'
 5 | import { Card, CardBody, CardHeader } from 'reactstrap'
 6 | 
 7 | export interface ScenarioLoaderCardProps extends CardProps {
 8 |   header: ReactNode
 9 |   children: ReactNode
10 | }
11 | 
12 | function ScenarioLoaderCard({
13 |   header,
14 |   children,
15 |   className,
16 |   ...restProps
17 | }: React.PropsWithChildren<ScenarioLoaderCardProps>) {
18 |   return (
19 |     <Card className={c('scenario-loader-card', className)} {...restProps}>
20 |       <CardHeader className="py-2">{header}</CardHeader>
21 |       <CardBody className="h-100">{children}</CardBody>
22 |     </Card>
23 |   )
24 | }
25 | 
26 | export { ScenarioLoaderCard }
27 | 


--------------------------------------------------------------------------------
/config/next/withPolyfills.ts:
--------------------------------------------------------------------------------
 1 | import { NextConfig } from 'next'
 2 | import { addWebpackConfig } from './lib/addWebpackConfig'
 3 | 
 4 | const POLYFILLS_FILE = './src/polyfills.ts'
 5 | 
 6 | export default function withPolyfills(nextConfig: NextConfig) {
 7 |   return addWebpackConfig(nextConfig, (nextConfig, webpackConfig, options) => {
 8 |     const originalEntry = webpackConfig.entry
 9 | 
10 |     webpackConfig.entry = async () => {
11 |       // eslint-disable-next-line @typescript-eslint/ban-ts-comment
12 |       // @ts-ignore
13 |       const entries = await originalEntry()
14 | 
15 |       if (entries['main.js'] && !entries['main.js'].includes(POLYFILLS_FILE)) {
16 |         entries['main.js'].unshift(POLYFILLS_FILE)
17 |       }
18 | 
19 |       return entries
20 |     }
21 | 
22 |     return webpackConfig
23 |   })
24 | }
25 | 


--------------------------------------------------------------------------------
/schemas/CaseCountsDatum.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: CaseCountsDatum
 3 | title: CaseCountsDatum
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - time
11 |   - cases
12 | 
13 | properties:
14 |   time:
15 |     type: string
16 |     format: date
17 | 
18 |   cases:
19 |     anyOf:
20 |       - $ref: 'IntegerNonNegative#'
21 |       - type: 'null'
22 | 
23 |   deaths:
24 |     anyOf:
25 |       - $ref: 'IntegerNonNegative#'
26 |       - type: 'null'
27 | 
28 |   hospitalized:
29 |     anyOf:
30 |       - $ref: 'IntegerNonNegative#'
31 |       - type: 'null'
32 | 
33 |   icu:
34 |     anyOf:
35 |       - $ref: 'IntegerNonNegative#'
36 |       - type: 'null'
37 | 
38 |   recovered:
39 |     anyOf:
40 |       - $ref: 'IntegerNonNegative#'
41 |       - type: 'null'
42 | 


--------------------------------------------------------------------------------
/src/assets/img/github.svg:
--------------------------------------------------------------------------------
1 | <svg role="img" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg"><title>GitHub icon</title><path d="M12 .297c-6.63 0-12 5.373-12 12 0 5.303 3.438 9.8 8.205 11.385.6.113.82-.258.82-.577 0-.285-.01-1.04-.015-2.04-3.338.724-4.042-1.61-4.042-1.61C4.422 18.07 3.633 17.7 3.633 17.7c-1.087-.744.084-.729.084-.729 1.205.084 1.838 1.236 1.838 1.236 1.07 1.835 2.809 1.305 3.495.998.108-.776.417-1.305.76-1.605-2.665-.3-5.466-1.332-5.466-5.93 0-1.31.465-2.38 1.235-3.22-.135-.303-.54-1.523.105-3.176 0 0 1.005-.322 3.3 1.23.96-.267 1.98-.399 3-.405 1.02.006 2.04.138 3 .405 2.28-1.552 3.285-1.23 3.285-1.23.645 1.653.24 2.873.12 3.176.765.84 1.23 1.91 1.23 3.22 0 4.61-2.805 5.625-5.475 5.92.42.36.81 1.096.81 2.22 0 1.606-.015 2.896-.015 3.286 0 .315.21.69.825.57C20.565 22.092 24 17.592 24 12.297c0-6.627-5.373-12-12-12"/></svg>


--------------------------------------------------------------------------------
/src/helpers/readFile.ts:
--------------------------------------------------------------------------------
 1 | export class FileReaderError extends Error {
 2 |   public readonly file: File
 3 |   constructor(file: File) {
 4 |     super(`Error: file "${file.name}" cannot be read.`)
 5 |     this.file = file
 6 |   }
 7 | }
 8 | 
 9 | export function readFile(file: File): Promise<string> {
10 |   const reader = new FileReader()
11 | 
12 |   return new Promise((resolve, reject) => {
13 |     reader.addEventListener('error', () => {
14 |       reader.abort()
15 |       reject(new FileReaderError(file))
16 |     })
17 | 
18 |     reader.addEventListener('load', () => {
19 |       const content = reader.result?.toString?.()
20 |       if (content) {
21 |         resolve(content)
22 |       } else {
23 |         reject(new FileReaderError(file))
24 |       }
25 |     })
26 | 
27 |     reader.readAsText(file)
28 |   })
29 | }
30 | 


--------------------------------------------------------------------------------
/src/state/settings/settings.state.ts:
--------------------------------------------------------------------------------
 1 | import { DEFAULT_LOCALE_KEY, LocaleKey } from '../../i18n/i18n'
 2 | 
 3 | export interface SettingsState {
 4 |   isAutorunEnabled: boolean
 5 |   shouldFormatNumbers: boolean
 6 |   selectShouldShowPlotLabels: boolean
 7 |   isLogScale: boolean
 8 |   areResultsMaximized: boolean
 9 |   disclaimerVersionAccepted?: number
10 |   disclaimerShouldSuppress: boolean
11 |   localeKey: LocaleKey
12 | }
13 | 
14 | export const settingsDefaultState: SettingsState = {
15 |   isAutorunEnabled: true,
16 |   shouldFormatNumbers: true,
17 |   selectShouldShowPlotLabels: false,
18 |   isLogScale: true,
19 |   areResultsMaximized: typeof window !== 'undefined' && window?.innerWidth > 2000,
20 |   disclaimerVersionAccepted: undefined,
21 |   disclaimerShouldSuppress: false,
22 |   localeKey: DEFAULT_LOCALE_KEY,
23 | }
24 | 


--------------------------------------------------------------------------------
/src/components/Form/SpinBox.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import classNames from 'classnames'
 4 | import { Field } from 'formik'
 5 | 
 6 | export interface FormSpinBoxProps extends React.HTMLProps<HTMLInputElement> {
 7 |   identifier: string
 8 |   step?: number | string
 9 |   min?: number
10 |   max?: number
11 |   pattern?: string
12 |   hasError?: boolean
13 | }
14 | 
15 | export function SpinBox({ identifier, step, min, max, pattern, hasError, ...restProps }: FormSpinBoxProps) {
16 |   return (
17 |     <Field
18 |       className={classNames('form-control', 'd-inline', hasError && 'border-danger')}
19 |       id={identifier}
20 |       name={identifier}
21 |       type="number"
22 |       step={step}
23 |       min={min}
24 |       max={max}
25 |       pattern={pattern}
26 |       {...restProps}
27 |     />
28 |   )
29 | }
30 | 


--------------------------------------------------------------------------------
/src/state/algorithm/algorithm.sagas.ts:
--------------------------------------------------------------------------------
 1 | import { SagaIterator } from 'redux-saga'
 2 | import { select, takeEvery } from 'redux-saga/effects'
 3 | import { RunParams } from '../../algorithms/run'
 4 | 
 5 | import { selectRunParams } from '../scenario/scenario.selectors'
 6 | import fsaSaga from '../util/fsaSaga'
 7 | 
 8 | import { algorithmRunAsync, AlgorithmRunResults, algorithmRunTrigger } from './algorithm.actions'
 9 | 
10 | import { run } from '../../workers/algorithm'
11 | 
12 | export function* workerAlgorithmRun(): SagaIterator | AlgorithmRunResults {
13 |   const params = (yield select(selectRunParams) as unknown) as RunParams
14 |   const result = (yield run(params) as unknown) as AlgorithmRunResults
15 |   return { result }
16 | }
17 | 
18 | export default [takeEvery(algorithmRunTrigger, fsaSaga(algorithmRunAsync, workerAlgorithmRun))]
19 | 


--------------------------------------------------------------------------------
/src/workers/algorithm/worker.ts:
--------------------------------------------------------------------------------
 1 | /* eslint-disable no-restricted-globals */
 2 | /* Necessary because 'self' should be accepted as a global in webworkers. */
 3 | 
 4 | import 'regenerator-runtime'
 5 | 
 6 | import { run, RunParams } from '../../algorithms/run'
 7 | 
 8 | self.addEventListener('message', (event: MessageEvent) => {
 9 |   const args = event.data as RunParams
10 | 
11 |   run(args)
12 |     .then((result) => self.postMessage({ result }))
13 |     .catch((error) => self.postMessage({ error: errorToString(error) }))
14 | })
15 | 
16 | /* Firefox cannot do structured cloning of Error types,
17 |  * therefore we convert the error into a string.
18 |  * Track https://bugzilla.mozilla.org/show_bug.cgi?id=1556604
19 |  */
20 | function errorToString(error: Error): string {
21 |   return `Algorithm error:${error.name}:${error.message}`
22 | }
23 | 


--------------------------------------------------------------------------------
/src/components/Form/FormCustom.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | import { Field } from 'formik'
 3 | import { Col, FormGroup, Row } from 'reactstrap'
 4 | import FormLabel from './FormLabel'
 5 | 
 6 | export interface FormCustomProps {
 7 |   children: React.ReactNode
 8 |   identifier: string
 9 |   label: string
10 |   help?: string | React.ReactNode
11 | }
12 | 
13 | export function FormCustom({ identifier, label, help, children }: FormCustomProps) {
14 |   return (
15 |     <Field>
16 |       {() => (
17 |         <FormGroup className="my-0">
18 |           <Row noGutters>
19 |             <Col xl={7}>
20 |               <FormLabel identifier={identifier} label={label} help={help} />
21 |             </Col>
22 |             <Col xl={5}>{children}</Col>
23 |           </Row>
24 |         </FormGroup>
25 |       )}
26 |     </Field>
27 |   )
28 | }
29 | 


--------------------------------------------------------------------------------
/src/components/Form/RangeSpinBox.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import { InputGroup } from 'reactstrap'
 4 | 
 5 | import { SpinBox } from './SpinBox'
 6 | 
 7 | export interface RangeSpinBoxProps {
 8 |   identifier: string
 9 |   step?: number | string
10 |   min?: number
11 |   max?: number
12 |   pattern?: string
13 |   hasError?: boolean
14 | }
15 | 
16 | export function RangeSpinBox({ identifier, step, min, max, pattern, hasError }: RangeSpinBoxProps) {
17 |   return (
18 |     <InputGroup>
19 |       <SpinBox identifier={`${identifier}.begin`} type="number" step={step} min={min} max={max} hasError={hasError} />
20 |       <span className="h-100 pt-2 px-1 text-bold">{' - '}</span>
21 |       <SpinBox identifier={`${identifier}.end`} type="number" step={step} min={min} max={max} hasError={hasError} />
22 |     </InputGroup>
23 |   )
24 | }
25 | 


--------------------------------------------------------------------------------
/src/components/Layout/Layout.tsx:
--------------------------------------------------------------------------------
 1 | import React, { PropsWithChildren, HTMLProps } from 'react'
 2 | 
 3 | import { Container } from 'reactstrap'
 4 | 
 5 | import { NavigationBar } from './NavigationBar'
 6 | import Footer from './Footer'
 7 | 
 8 | export function Layout({ children }: PropsWithChildren<HTMLProps<HTMLDivElement>>) {
 9 |   return (
10 |     <Container fluid className="layout-container px-0">
11 |       <header className="row navbar-container d-print-none">
12 |         <NavigationBar />
13 |       </header>
14 | 
15 |       <div className="row main-wrapper">
16 |         <main className="main container-fluid absolute" role="main">
17 |           {children}
18 |         </main>
19 |       </div>
20 | 
21 |       <footer className="row d-print-none footer">
22 |         <Footer />
23 |       </footer>
24 |     </Container>
25 |   )
26 | }
27 | 


--------------------------------------------------------------------------------
/src/io/defaults/__tests__/getCaseCountsData.test.ts:
--------------------------------------------------------------------------------
 1 | import { getCaseCountsData } from '../getCaseCountsData'
 2 | 
 3 | describe('getSortedNonEmptyCaseCounts', () => {
 4 |   it('sorts by ascending time', () => {
 5 |     const got = getCaseCountsData('United States of America').data
 6 |     got.forEach((entry, index) => {
 7 |       if (index > 0) {
 8 |         // eslint-disable-next-line jest/no-conditional-expect
 9 |         expect(entry.time.getTime()).toBeGreaterThan(got[index - 1].time.getTime())
10 |       }
11 |     })
12 |   })
13 | 
14 |   it('returns no empty entries', () => {
15 |     const got = getCaseCountsData('United States of America').data
16 |     got.forEach((entry) => {
17 |       const notEmpty = entry.cases || entry.deaths || entry.icu || entry.hospitalized
18 |       expect(notEmpty).toBeTruthy()
19 |     })
20 |   })
21 | })
22 | 


--------------------------------------------------------------------------------
/src/state/algorithm/algorithm.reducer.ts:
--------------------------------------------------------------------------------
 1 | import { reducerWithInitialState } from 'typescript-fsa-reducers'
 2 | 
 3 | import immerCase from '../util/fsaImmerReducer'
 4 | import { algorithmRunAsync } from './algorithm.actions'
 5 | import { defaultAlgorithmState } from './algorithm.state'
 6 | 
 7 | export const algorithmReducer = reducerWithInitialState(defaultAlgorithmState) // prettier-ignore
 8 |   .withHandling(
 9 |     immerCase(algorithmRunAsync.started, (draft) => {
10 |       draft.isRunning = true
11 |     }),
12 |   )
13 | 
14 |   .withHandling(
15 |     immerCase(algorithmRunAsync.done, (draft, { result }) => {
16 |       draft.isRunning = false
17 |       draft.result = result.result
18 |     }),
19 |   )
20 | 
21 |   .withHandling(
22 |     immerCase(algorithmRunAsync.failed, (draft) => {
23 |       draft.isRunning = false
24 |     }),
25 |   )
26 | 


--------------------------------------------------------------------------------
/src/helpers/getVersionString.ts:
--------------------------------------------------------------------------------
 1 | export function getVersionString() {
 2 |   const BRANCH_NAME = process.env.BRANCH_NAME ?? ''
 3 |   const PACKAGE_VERSION = process.env.PACKAGE_VERSION ?? ''
 4 |   const REVISION = process.env.REVISION ?? ''
 5 |   const BUILD_NUMBER = process.env.BUILD_NUMBER ?? ''
 6 | 
 7 |   let version = PACKAGE_VERSION
 8 |   let meta: string[] = []
 9 |   if (REVISION && REVISION.length >= 7) {
10 |     meta = [...meta, `rev: ${REVISION.slice(0, 7)}`]
11 |   }
12 | 
13 |   if (BUILD_NUMBER) {
14 |     meta = [...meta, `build: ${BUILD_NUMBER}`]
15 |   }
16 | 
17 |   if (BRANCH_NAME && !BRANCH_NAME.startsWith('prod')) {
18 |     meta = [...meta, `env: ${BRANCH_NAME}`]
19 |   }
20 | 
21 |   const metaStr = meta.join(', ')
22 |   if (metaStr.length > 0) {
23 |     version = `version ${version} (${metaStr})`
24 |   }
25 | 
26 |   return version
27 | }
28 | 


--------------------------------------------------------------------------------
/.github/workflows/eslint.yml:
--------------------------------------------------------------------------------
 1 | name: eslint
 2 | 
 3 | on:
 4 |   - pull_request
 5 | 
 6 | jobs:
 7 |   eslint:
 8 |     runs-on: ubuntu-18.04
 9 |     steps:
10 |       - uses: actions/checkout@v2
11 | 
12 |       - uses: actions/setup-node@v1
13 |         with:
14 |           node-version: 12.x
15 | 
16 |       - run: yarn install
17 | 
18 |       - run: yarn schema:totypes
19 | 
20 |       - uses: reviewdog/action-eslint@v1
21 |         with:
22 |           github_token: ${{ secrets.GITHUB_TOKEN }}
23 |           eslint_flags: '**/*.{js,jsx,ts,tsx} --max-warnings=0'
24 |           fail_on_error: true
25 | 
26 |       - uses: reviewdog/action-eslint@v1
27 |         with:
28 |           github_token: ${{ secrets.GITHUB_TOKEN }}
29 |           reporter: github-pr-review
30 |           eslint_flags: '**/*.{js,jsx,ts,tsx} --max-warnings=0'
31 |           fail_on_error: true
32 | 


--------------------------------------------------------------------------------
/config/nodemon/eslint.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "quiet": true,
 3 |   "legacyWatch": false,
 4 |   "delay": 0.1,
 5 |   "watch": [
 6 |     "../.env",
 7 |     ".browserslistrc",
 8 |     ".editorconfig",
 9 |     ".env",
10 |     ".eslintignore",
11 |     ".eslintrc.js",
12 |     ".prettierignore",
13 |     ".prettierrc",
14 |     "babel.config.js",
15 |     "config",
16 |     "cypress",
17 |     "jest.config.js",
18 |     "package.json",
19 |     "postcss.config.js",
20 |     "src",
21 |     "stylelint.config.js",
22 |     "tsconfig.json",
23 |     "webpack.config.js",
24 |     "yarn.lock"
25 |   ],
26 |   "ext": "js,jsx,ts,tsx,json,flow,css,scss,sass,styl,html,ejs,d,txt,yml,sh",
27 |   "ignore": ["**/*.test.*s", "**/*.test.*sx", "**/__tests__", ".build", "config/jest", "node_modules"],
28 |   "exec": "yarn clear && yarn eslint && echo '\u2714 OK' || echo '\u274C FAILED' || cd ."
29 | }
30 | 


--------------------------------------------------------------------------------
/config/nodemon/eslint.fix.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "quiet": true,
 3 |   "legacyWatch": false,
 4 |   "delay": 0.1,
 5 |   "watch": [
 6 |     "../.env",
 7 |     ".browserslistrc",
 8 |     ".editorconfig",
 9 |     ".env",
10 |     ".eslintignore",
11 |     ".eslintrc.js",
12 |     ".prettierignore",
13 |     ".prettierrc",
14 |     "babel.config.js",
15 |     "config",
16 |     "cypress",
17 |     "jest.config.js",
18 |     "package.json",
19 |     "postcss.config.js",
20 |     "src",
21 |     "stylelint.config.js",
22 |     "tsconfig.json",
23 |     "webpack.config.js",
24 |     "yarn.lock"
25 |   ],
26 |   "ext": "js,jsx,ts,tsx,json,flow,css,scss,sass,styl,html,ejs,d,txt,yml,sh",
27 |   "ignore": ["**/*.test.*s", "**/*.test.*sx", "**/__tests__", ".build", "config/jest", "node_modules"],
28 |   "exec": "yarn clear && yarn eslint:fix && echo '\u2714 OK' || echo '\u274C FAILED' || cd ."
29 | }
30 | 


--------------------------------------------------------------------------------
/docker/docker-compose.dev.yml:
--------------------------------------------------------------------------------
 1 | version: '3.7'
 2 | 
 3 | services:
 4 |   covid19_scenarios-dev-web:
 5 |     container_name: covid19_scenarios-dev-web
 6 |     image: covid19_scenarios-dev-web
 7 |     build:
 8 |       context: ./
 9 |       dockerfile: node-git-alpine/Dockerfile
10 |     command: sh -c "cd /code && yarn install --silent && yarn dev"
11 |     volumes:
12 |       - ../:/code
13 |       - /etc/timezone:/etc/timezone:ro
14 |       - /etc/localtime:/etc/localtime:ro
15 |     ports:
16 |       - 3000:3000
17 |     environment:
18 |       - COLORTERM=truecolor
19 |       - TERM=xterm-truecolor
20 |     restart: 'no'
21 |     init: true
22 |     user: '${UID}'
23 |     tty: true
24 | 
25 |     networks:
26 |       - network-covid19_scenarios-dev
27 | 
28 | networks:
29 |   network-covid19_scenarios-dev:
30 |     ipam:
31 |       config:
32 |         - subnet: 172.16.239.0/24
33 | 


--------------------------------------------------------------------------------
/src/styles/components/ScenarioTitle.scss:
--------------------------------------------------------------------------------
 1 | @import '../variables';
 2 | 
 3 | .scenario-title-input {
 4 |   min-height: 70px;
 5 |   overflow: hidden;
 6 |   font-size: 1.5em;
 7 |   font-weight: bold;
 8 |   text-overflow: ellipsis;
 9 |   white-space: nowrap;
10 | 
11 |   &:read-only {
12 |     background-color: $body-background;
13 |     border-color: transparent;
14 |     box-shadow: none;
15 |   }
16 | }
17 | 
18 | .scenario-title-input-group {
19 |   border-color: transparent;
20 |   box-shadow: none;
21 | }
22 | 
23 | .scenario-title-btn {
24 |   background-color: transparent;
25 |   border-color: transparent;
26 |   box-shadow: none;
27 | }
28 | 
29 | .scenario-title-icon {
30 |   font-size: 1.5em;
31 |   fill: $gray-600;
32 | 
33 |   &.scenario-title-icon-cancel {
34 |     fill: $danger;
35 |   }
36 | 
37 |   &.scenario-title-icon-confirm {
38 |     fill: $success;
39 |   }
40 | }
41 | 


--------------------------------------------------------------------------------
/config/next/withLodash.ts:
--------------------------------------------------------------------------------
 1 | import type { NextConfig } from 'next'
 2 | import LodashWebpackPlugin, { Options } from 'lodash-webpack-plugin'
 3 | 
 4 | import { addWebpackPlugin } from './lib/addWebpackPlugin'
 5 | 
 6 | const withLodash = (options: Options) => (nextConfig: NextConfig) => {
 7 |   return addWebpackPlugin(
 8 |     nextConfig,
 9 |     new LodashWebpackPlugin({
10 |       caching: true,
11 |       chaining: true,
12 |       cloning: true,
13 |       coercions: true,
14 |       collections: true,
15 |       currying: true,
16 |       deburring: true,
17 |       exotics: true,
18 |       flattening: true,
19 |       guards: true,
20 |       memoizing: true,
21 |       metadata: true,
22 |       paths: true,
23 |       placeholders: true,
24 |       shorthands: true,
25 |       unicode: true,
26 |       ...options,
27 |     }),
28 |   )
29 | }
30 | 
31 | export default withLodash
32 | 


--------------------------------------------------------------------------------
/src/io/encoding/decode.ts:
--------------------------------------------------------------------------------
 1 | import queryString from 'query-string'
 2 | 
 3 | import { head } from 'lodash'
 4 | 
 5 | import { ErrorURLDecoderVersionInvalid } from './errors'
 6 | import { URL_ENCODER_VERSIONS, URL_ENCODERS } from './versioning'
 7 | 
 8 | export function first<T>(a: T | T[]) {
 9 |   return Array.isArray(a) ? head(a) : a
10 | }
11 | 
12 | export function decode(url: string) {
13 |   const params = queryString.parse(url)
14 |   const v = first(params?.v)
15 |   const q = first(params?.q)
16 | 
17 |   if (!q) {
18 |     return null
19 |   }
20 | 
21 |   if (v) {
22 |     const decodeVersioned = URL_ENCODERS.get(v)?.decode
23 |     if (!decodeVersioned) {
24 |       throw new ErrorURLDecoderVersionInvalid(v, URL_ENCODER_VERSIONS)
25 |     }
26 |     return decodeVersioned(q)
27 |   }
28 | 
29 |   throw new ErrorURLDecoderVersionInvalid('Not provided', URL_ENCODER_VERSIONS)
30 | }
31 | 


--------------------------------------------------------------------------------
/src/algorithms/utils/suggestNextMitigationInterval.ts:
--------------------------------------------------------------------------------
 1 | import moment from 'moment'
 2 | 
 3 | import createColor from 'create-color'
 4 | import type { StrictOmit } from 'ts-essentials'
 5 | import { uuidv4 } from '../../helpers/uuid'
 6 | 
 7 | import type { MitigationInterval } from '../types/Param.types'
 8 | 
 9 | export function suggestNextMitigationInterval(): MitigationInterval {
10 |   const tMinMoment = moment()
11 |   const tMaxMoment = tMinMoment.clone().add(30, 'days')
12 | 
13 |   const timeRange = { begin: moment().toDate(), end: tMaxMoment.toDate() }
14 | 
15 |   const interval: StrictOmit<MitigationInterval, 'color'> = {
16 |     id: uuidv4(),
17 |     name: `Intervention from ${tMinMoment.format('D MMM YYYY')}`,
18 |     timeRange,
19 |     transmissionReduction: { begin: 10, end: 30 },
20 |   }
21 | 
22 |   const color = createColor(interval)
23 | 
24 |   return { ...interval, color }
25 | }
26 | 


--------------------------------------------------------------------------------
/config/nodemon/analyze.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "quiet": true,
 3 |   "legacyWatch": false,
 4 |   "delay": 0.1,
 5 |   "watch": [
 6 |     "../.env",
 7 |     ".browserslistrc",
 8 |     ".editorconfig",
 9 |     ".env",
10 |     ".eslintignore",
11 |     ".eslintrc.js",
12 |     ".prettierignore",
13 |     ".prettierrc",
14 |     "babel.config.js",
15 |     "config",
16 |     "package.json",
17 |     "postcss.config.js",
18 |     "schemas",
19 |     "src",
20 |     "stylelint.config.js",
21 |     "tsconfig.json",
22 |     "webpack.config.js",
23 |     "yarn.lock"
24 |   ],
25 |   "ext": "js,jsx,ts,tsx,json,flow,css,scss,sass,styl,html,ejs,d,txt,yml,sh",
26 |   "ignore": [
27 |     "**/*.test.*s",
28 |     "**/*.test.*sx",
29 |     "**/__tests__",
30 |     ".build",
31 |     "config/jest",
32 |     "node_modules",
33 |     "src/.generated"
34 |   ],
35 |   "exec": "yarn clear && yarn install && yarn analyze || cd ."
36 | }
37 | 


--------------------------------------------------------------------------------
/config/nodemon/prod.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "quiet": true,
 3 |   "legacyWatch": false,
 4 |   "delay": 0.1,
 5 |   "watch": [
 6 |     "../.env",
 7 |     ".browserslistrc",
 8 |     ".editorconfig",
 9 |     ".env",
10 |     ".eslintignore",
11 |     ".eslintrc.js",
12 |     ".prettierignore",
13 |     ".prettierrc",
14 |     "babel.config.js",
15 |     "config",
16 |     "package.json",
17 |     "postcss.config.js",
18 |     "schemas",
19 |     "src",
20 |     "static",
21 |     "stylelint.config.js",
22 |     "tsconfig.json",
23 |     "webpack.config.js",
24 |     "yarn.lock"
25 |   ],
26 |   "ext": "js,jsx,ts,tsx,json,flow,css,scss,sass,styl,html,ejs,d,txt,yml,sh",
27 |   "ignore": [
28 |     "**/*.test.*s",
29 |     "**/*.test.*sx",
30 |     "**/__tests__",
31 |     ".build",
32 |     "config/jest",
33 |     "node_modules",
34 |     "src/.generated"
35 |   ],
36 |   "exec": "run-s -c clear prod:clean prod:start || cd ."
37 | }
38 | 


--------------------------------------------------------------------------------
/config/next/withSvg.ts:
--------------------------------------------------------------------------------
 1 | import type { NextConfig } from 'next'
 2 | 
 3 | import { addWebpackLoader } from './lib/addWebpackLoader'
 4 | 
 5 | export default function withSvg(nextConfig: NextConfig) {
 6 |   return addWebpackLoader(nextConfig, (webpackConfig, { dev }) => ({
 7 |     // eslint-disable-next-line security/detect-unsafe-regex
 8 |     test: /\.svg(\?.*)?$/i,
 9 |     use: [
10 |       {
11 |         loader: '@svgr/webpack',
12 |         options: {
13 |           svgoConfig: {
14 |             plugins: [
15 |               {
16 |                 removeViewBox: false,
17 |               },
18 |             ],
19 |           },
20 |         },
21 |       },
22 |       {
23 |         loader: 'url-loader',
24 |         options: {
25 |           limit: false,
26 |           name: dev ? '[name].[ext]' : '[name].[hash:7].[ext]',
27 |           publicPath: 'assets',
28 |         },
29 |       },
30 |     ],
31 |   }))
32 | }
33 | 


--------------------------------------------------------------------------------
/src/helpers/getFormikErrors.ts:
--------------------------------------------------------------------------------
 1 | import { get, isEmpty } from 'lodash'
 2 | 
 3 | import { FormikErrors, FormikTouched, FormikValues } from 'formik'
 4 | 
 5 | export interface GetErrorParams {
 6 |   identifier: string
 7 |   errors?: FormikErrors<FormikValues>
 8 |   touched?: FormikTouched<FormikValues> | true
 9 | }
10 | 
11 | export function getFormikErrors({ identifier, errors, touched }: GetErrorParams): string[] {
12 |   // const isTouched = (typeof touched === 'boolean' && touched === true) || get(touched, identifier)
13 |   const errorMessage = get(errors, identifier)
14 | 
15 |   if (!errorMessage || isEmpty(errorMessage) /* || !isTouched */) {
16 |     return []
17 |   }
18 | 
19 |   if (typeof errorMessage === 'string') {
20 |     return [errorMessage]
21 |   }
22 | 
23 |   if (Array.isArray(errorMessage)) {
24 |     return errorMessage as string[]
25 |   }
26 | 
27 |   return Object.values(errorMessage) as string[]
28 | }
29 | 


--------------------------------------------------------------------------------
/now.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "rewrites": [{ "source": "/(.*)", "destination": "/index.html" }],
 3 |   "builds": [
 4 |     {
 5 |       "use": "@vercel/static-build",
 6 |       "src": "package.json",
 7 |       "config": { "distDir": ".build/production/web" }
 8 |     }
 9 |   ],
10 |   "build": {
11 |     "env": {
12 |       "WEB_SCHEMA": "http",
13 |       "WEB_HOST": "null",
14 |       "WEB_PORT_DEV": "3000",
15 |       "WEB_PORT_PROD": "null",
16 |       "WEB_PORT_ANALYZE": "8888",
17 | 
18 |       "NEXT_TELEMETRY_DISABLED": "0",
19 | 
20 |       "DEV_ENABLE_TYPE_CHECKS": "1",
21 |       "DEV_ENABLE_ESLINT": "1",
22 |       "DEV_ENABLE_STYLELINT": "1",
23 |       "DEV_ENABLE_REDUX_DEV_TOOLS": "1",
24 |       "DEV_ENABLE_REDUX_IMMUTABLE_STATE_INVARIANT": "0",
25 | 
26 |       "PROD_ENABLE_SOURCE_MAPS": "1",
27 |       "PROD_ENABLE_REDUX_DEV_TOOLS": "1",
28 |       "PROD_ENABLE_REDUX_IMMUTABLE_STATE_INVARIANT": "0"
29 |     }
30 |   }
31 | }
32 | 


--------------------------------------------------------------------------------
/src/components/Form/FormHelpButton.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | import { Card, CardBody } from 'reactstrap'
 3 | 
 4 | import { useTranslationSafe } from 'src/helpers/useTranslationSafe'
 5 | import Popover from '../Wrappers/Popover'
 6 | 
 7 | export interface FormHelpButtonProps {
 8 |   help?: string | React.ReactNode
 9 | }
10 | 
11 | export default function FormHelpButton({ help }: FormHelpButtonProps) {
12 |   const { t } = useTranslationSafe()
13 | 
14 |   return (
15 |     <Popover preventDefault stopPropagation style={{ border: 'none' }}>
16 |       <button className="btn btn-secondary help-button ml-2" type="button" title={t('Click to get help')}>
17 |         <span className="help-button-icon">{'?'}</span>
18 |       </button>
19 |       <Card className="card-help">
20 |         <CardBody className="card-body-help">
21 |           <p>{help}</p>
22 |         </CardBody>
23 |       </Card>
24 |     </Popover>
25 |   )
26 | }
27 | 


--------------------------------------------------------------------------------
/src/components/Form/FormSwitch.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import { CustomInput } from 'reactstrap'
 4 | 
 5 | import FormLabel from './FormLabel'
 6 | 
 7 | export interface FormSwitchProps {
 8 |   identifier: string
 9 |   label: string
10 |   help?: string
11 |   checked: boolean
12 |   hidden?: boolean
13 |   onValueChanged(checked: boolean): void
14 | }
15 | 
16 | export default function FormSwitch({
17 |   identifier,
18 |   label,
19 |   help,
20 |   onValueChanged,
21 |   checked,
22 |   hidden = false,
23 |   ...props
24 | }: FormSwitchProps) {
25 |   return (
26 |     <CustomInput
27 |       type="checkbox"
28 |       className="custom-switch"
29 |       id={identifier}
30 |       name={identifier}
31 |       label={<FormLabel identifier={identifier} label={label} help={help} />}
32 |       checked={checked}
33 |       onChange={(e) => onValueChanged(e.target.checked)}
34 |       {...props}
35 |     />
36 |   )
37 | }
38 | 


--------------------------------------------------------------------------------
/lib/getGitBranch.ts:
--------------------------------------------------------------------------------
 1 | import { execSync } from 'child_process'
 2 | 
 3 | import { getenv } from './getenv'
 4 | 
 5 | export function getGitCommitHashLocal() {
 6 |   try {
 7 |     return execSync('git rev-parse --abbrev-ref HEAD').toString().trim()
 8 |   } catch {
 9 |     return undefined
10 |   }
11 | }
12 | 
13 | export function getGitBranch() {
14 |   return (
15 |     getenv('GIT_BRANCH', null) ??
16 |     getenv('BRANCH', null) ??
17 |     getenv('TRAVIS_BRANCH', null) ??
18 |     getenv('NOW_GITHUB_COMMIT_REF', null) ??
19 |     getenv('VERCEL_GITHUB_COMMIT_REF', null) ??
20 |     getenv('VERCEL_GITLAB_COMMIT_REF', null) ??
21 |     getenv('VERCEL_BITBUCKET_COMMIT_REF', null) ??
22 |     getenv('ZEIT_GITHUB_COMMIT_REF', null) ??
23 |     getenv('ZEIT_GITLAB_COMMIT_REF', null) ??
24 |     getenv('ZEIT_BITBUCKET_COMMIT_REF', null) ??
25 |     getenv('CIRCLE_BRANCH', null) ??
26 |     getGitCommitHashLocal() ??
27 |     ''
28 |   )
29 | }
30 | 


--------------------------------------------------------------------------------
/src/state/ui/ui.sagas.ts:
--------------------------------------------------------------------------------
 1 | import { select, takeEvery, put } from 'redux-saga/effects'
 2 | 
 3 | import { push } from 'connected-next-router'
 4 | import urlJoin from 'proper-url-join'
 5 | 
 6 | import type { ScenarioParameters } from '../../algorithms/types/Param.types'
 7 | import { toUrl } from '../../io/serialization/toUrl'
 8 | import { selectScenarioParameters } from '../scenario/scenario.selectors'
 9 | import { newTabOpenTrigger, printPreviewOpenTrigger } from './ui.actions'
10 | 
11 | export function* newTabOpen() {
12 |   const data = ((yield select(selectScenarioParameters)) as unknown) as ScenarioParameters
13 |   const scenarioUrl = decodeURI(urlJoin(window?.location.href, toUrl(data)))
14 |   window?.open(scenarioUrl, '_blank')
15 | }
16 | 
17 | export function* printPreviewOpen() {
18 |   yield put(push('/print'))
19 | }
20 | 
21 | export default [takeEvery(newTabOpenTrigger, newTabOpen), takeEvery(printPreviewOpenTrigger, printPreviewOpen)]
22 | 


--------------------------------------------------------------------------------
/config/next/withImages.ts:
--------------------------------------------------------------------------------
 1 | import type { NextConfig } from 'next'
 2 | 
 3 | import { addWebpackLoader } from './lib/addWebpackLoader'
 4 | 
 5 | export default function withSvg(nextConfig: NextConfig) {
 6 |   return addWebpackLoader(nextConfig, (webpackConfig, { dev, isServer }) => ({
 7 |     test: /\.(gif|ico|jp2|jpe?g|png|webp)$/,
 8 |     issuer: {
 9 |       // Next.js already handles url() in css/sass/scss files
10 |       // eslint-disable-next-line security/detect-unsafe-regex
11 |       test: /\.\w+(?<!(s?c|sa)ss)$/i,
12 |     },
13 |     exclude: nextConfig.exclude,
14 |     use: [
15 |       {
16 |         loader: 'url-loader',
17 |         options: {
18 |           limit: false,
19 |           name: dev ? '[name].[ext]' : '[name].[hash:7].[ext]',
20 |           publicPath: `${nextConfig.assetPrefix}/_next/static/images/`,
21 |           outputPath: `${isServer ? '../' : ''}static/images/`,
22 |         },
23 |       },
24 |     ],
25 |   }))
26 | }
27 | 


--------------------------------------------------------------------------------
/lib/getGitCommitHash.ts:
--------------------------------------------------------------------------------
 1 | import { execSync } from 'child_process'
 2 | 
 3 | import { getenv } from './getenv'
 4 | 
 5 | export function getGitCommitHashLocal() {
 6 |   try {
 7 |     return execSync('git rev-parse HEAD').toString().trim()
 8 |   } catch {
 9 |     return undefined
10 |   }
11 | }
12 | 
13 | export function getGitCommitHash() {
14 |   return (
15 |     getenv('GIT_COMMIT', null) ??
16 |     getenv('GIT_COMMIT_HASH', null) ??
17 |     getenv('TRAVIS_COMMIT', null) ??
18 |     getenv('NOW_GITHUB_COMMIT_SHA', null) ??
19 |     getenv('GITHUB_SHA', null) ??
20 |     getenv('COMMIT_REF', null) ??
21 |     getenv('VERCEL_GITHUB_COMMIT_SHA', null) ??
22 |     getenv('VERCEL_GITLAB_COMMIT_SHA', null) ??
23 |     getenv('VERCEL_BITBUCKET_COMMIT_SHA', null) ??
24 |     getenv('ZEIT_GITHUB_COMMIT_SHA', null) ??
25 |     getenv('ZEIT_GITLAB_COMMIT_SHA', null) ??
26 |     getenv('ZEIT_BITBUCKET_COMMIT_SHA', null) ??
27 |     getGitCommitHashLocal()
28 |   )
29 | }
30 | 


--------------------------------------------------------------------------------
/schemas/ScenarioDatumPopulation.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: ScenarioDatumPopulation
 3 | title: ScenarioDatumPopulation
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - populationServed
11 |   - seroprevalence
12 |   - ageDistributionName
13 |   - caseCountsName
14 |   - initialNumberOfCases
15 |   - importsPerDay
16 |   - hospitalBeds
17 |   - icuBeds
18 | 
19 | properties:
20 |   populationServed:
21 |     $ref: 'IntegerNonNegative#'
22 | 
23 |   seroprevalence:
24 |     $ref: 'Percentage#'
25 | 
26 |   ageDistributionName:
27 |     type: string
28 |     minLength: 1
29 | 
30 |   caseCountsName:
31 |     type: string
32 |     minLength: 1
33 | 
34 |   initialNumberOfCases:
35 |     $ref: 'IntegerNonNegative#'
36 | 
37 |   importsPerDay:
38 |     type: number
39 |     minimum: 0
40 | 
41 |   hospitalBeds:
42 |     $ref: 'IntegerNonNegative#'
43 | 
44 |   icuBeds:
45 |     $ref: 'IntegerNonNegative#'
46 | 


--------------------------------------------------------------------------------
/src/types/formik.d.ts:
--------------------------------------------------------------------------------
 1 | declare module 'formik' {
 2 |   import type { FieldHookConfig } from 'formik/dist/Field'
 3 |   import type { FormikErrors, FieldHelperProps, FieldInputProps, FormikTouched } from 'formik/dist/types'
 4 | 
 5 |   export * from 'formik/dist/index'
 6 | 
 7 |   export interface FieldMetaProps<Value> {
 8 |     /** Value of the field */
 9 |     value: Value
10 |     /** Error message of the field */
11 |     error?: FormikErrors<Value>
12 |     /** Has the field been visited? */
13 |     touched: FormikTouched<Value>
14 |     /** Initial value of the field */
15 |     initialValue?: Value
16 |     /** Initial touched state of the field */
17 |     initialTouched: boolean
18 |     /** Initial error message of the field */
19 |     initialError?: string
20 |   }
21 | 
22 |   export declare function useField<Val = any>(
23 |     propsOrFieldName: string | FieldHookConfig<Val>,
24 |   ): [FieldInputProps<Val>, FieldMetaProps<Val>, FieldHelperProps<Val>]
25 | }
26 | 


--------------------------------------------------------------------------------
/src/components/Main/CaseCounts/CaseCountsUploaderInstructionsText.mdx:
--------------------------------------------------------------------------------
 1 | Here you can import custom Case Counts data to display alongside the results of the simulation. Case counts are
 2 | displayed as dots on the trajectories plot. This allows to compare the results of the model with real-world statistics.
 3 | 
 4 | The uploaded files are expected in CSV (comma-separated values) or TSV (tab-separated values) format. You can check out
 5 | some concrete examples of case counts files in our data directory, for example:
 6 | [USA-New York.tsv](https://github.com/neherlab/covid19_scenarios/blob/release/data/case-counts/unitedstates/USA-New%20York.tsv)
 7 | 
 8 | After internal conversion, each row will be validated according to this JSON schema:
 9 | [CaseCountsDatum.yml](https://github.com/neherlab/covid19_scenarios/blob/release/schemas/CaseCountsDatum.yml).
10 | 
11 | You can omit the missing values. But don't forget to put the appropriate number of columns (with consecutive tabs or commas).
12 | 


--------------------------------------------------------------------------------
/src/styles/components/OutcomesDetailsTable.scss:
--------------------------------------------------------------------------------
 1 | @import '../variables';
 2 | @import '../mixins';
 3 | 
 4 | @media not print {
 5 |   .outcomes-table-wrapper {
 6 |     &:not(.print-preview) {
 7 |       height: 500px;
 8 |       overflow: auto;
 9 |     }
10 |   }
11 | 
12 |   .outcomes-table {
13 |     &:not(.print-preview) {
14 |       min-width: 800px;
15 |       table-layout: fixed;
16 |     }
17 | 
18 |     th,
19 |     td,
20 |     tr {
21 |       text-align: center;
22 |       vertical-align: middle;
23 |     }
24 |   }
25 | 
26 |   .outcome-table-th {
27 |     text-align: center;
28 |   }
29 | 
30 |   .outcome-table-th-date {
31 |     width: 9rem;
32 |   }
33 | }
34 | 
35 | .bg-severe {
36 |   background-color: #fb9a991a;
37 | }
38 | 
39 | .bg-critical {
40 |   background-color: #e31a1c1a;
41 | }
42 | 
43 | .bg-overflow {
44 |   background-color: #900d2c1a;
45 | }
46 | 
47 | .bg-fatality {
48 |   background-color: #5e506a1a;
49 | }
50 | 
51 | .bg-recovered {
52 |   background-color: #33a02c1a;
53 | }
54 | 


--------------------------------------------------------------------------------
/src/io/encoding/versioning.ts:
--------------------------------------------------------------------------------
 1 | import { last } from 'lodash'
 2 | 
 3 | import type { ScenarioParameters } from '../../algorithms/types/Param.types'
 4 | 
 5 | import { getOrThrow } from '../../helpers/getOrThrow'
 6 | 
 7 | import urlv1 from './v1/encode'
 8 | 
 9 | export type Serializer = (input: ScenarioParameters) => string
10 | export type Deserializer = (input: string) => ScenarioParameters
11 | 
12 | export type UrlEncoder = (obj: Record<string, unknown>) => string
13 | export type UrlDecoder = (str: string) => Record<string, unknown>
14 | 
15 | export interface UrlEncoders {
16 |   encode: UrlEncoder
17 |   decode: UrlDecoder
18 | }
19 | 
20 | export const URL_ENCODERS = new Map<string, UrlEncoders>(
21 |   Object.entries({
22 |     '1': urlv1,
23 |   }),
24 | )
25 | export const URL_ENCODER_VERSIONS = Array.from(URL_ENCODERS.keys()).sort()
26 | export const URL_ENCODER_VERSION_LATEST = last(URL_ENCODER_VERSIONS) ?? '1'
27 | export const URL_ENCODER_LATEST = getOrThrow(URL_ENCODERS, URL_ENCODER_VERSION_LATEST)
28 | 


--------------------------------------------------------------------------------
/docker/docker-compose.data.yml:
--------------------------------------------------------------------------------
 1 | version: '3.7'
 2 | 
 3 | services:
 4 |   covid19_scenarios-dev-web:
 5 |     container_name: covid19_scenarios-dev-data
 6 |     image: ovid19_scenarios-dev-data
 7 |     build:
 8 |       context: ./
 9 |       dockerfile: python-pip/Dockerfile
10 |     working_dir: /code/data
11 |     command: bash -c "cd /code/data && make data-for-app"
12 |     volumes:
13 |       - ../:/code
14 |       - ../.cache/data/.cache:/.cache
15 |       - ../.cache/data/.local/bin:/.local/bin
16 |       - ../.cache/data/.local/share:/.local/share
17 |       - /etc/timezone:/etc/timezone:ro
18 |       - /etc/localtime:/etc/localtime:ro
19 |     environment:
20 |       - COLORTERM=truecolor
21 |       - TERM=xterm-truecolor
22 |     restart: 'no'
23 |     init: true
24 |     user: '${UID}'
25 |     tty: true
26 | 
27 |     networks:
28 |       - network-covid19_scenarios-dev-data
29 | 
30 | networks:
31 |   network-covid19_scenarios-dev-data:
32 |     ipam:
33 |       config:
34 |         - subnet: 172.16.238.0/24
35 | 


--------------------------------------------------------------------------------
/src/state/settings/settings.actions.ts:
--------------------------------------------------------------------------------
 1 | import actionCreatorFactory from 'typescript-fsa'
 2 | 
 3 | import type { LocaleKey } from '../../i18n/i18n'
 4 | 
 5 | const action = actionCreatorFactory('SETTINGS')
 6 | 
 7 | export const toggleAutorun = action('TOGGLE_AUTORUN')
 8 | export const toggleLogScale = action('TOGGLE_LOG_SCALE')
 9 | export const toggleFormatNumbers = action('TOGGLE_FORMAT_NUMBERS')
10 | export const toggleResultsMaximized = action('TOGGLE_RESULTS_MAXIMIZED')
11 | 
12 | export const setAutorun = action<boolean>('SET_AUTORUN')
13 | export const setLogScale = action<boolean>('SET_LOG_SCALE')
14 | export const setFormatNumbers = action<boolean>('SET_FORMAT_NUMBERS')
15 | export const setResultsMaximized = action<boolean>('SET_RESULTS_MAXIMIZED')
16 | 
17 | export const setDisclaimerVersionAccepted = action<number>('SET_DISCLAIMER_VERSION_ACCEPTED')
18 | export const toggleDisclaimerShouldSuppress = action('TOGGLE_DISCLAIMER_SHOULD_SUPPRESS')
19 | 
20 | export const setLocale = action<LocaleKey>('SET_LOCALE')
21 | 


--------------------------------------------------------------------------------
/schemas/ScenarioDatumEpidemiological.yml:
--------------------------------------------------------------------------------
 1 | $schema: http://json-schema.org/draft-07/schema
 2 | $id: ScenarioDatumEpidemiological
 3 | title: ScenarioDatumEpidemiological
 4 | 
 5 | type: object
 6 | 
 7 | additionalProperties: false
 8 | 
 9 | required:
10 |   - r0
11 |   - latencyDays
12 |   - infectiousPeriodDays
13 |   - hospitalStayDays
14 |   - icuStayDays
15 |   - seasonalForcing
16 |   - peakMonth
17 |   - overflowSeverity
18 | 
19 | properties:
20 |   r0:
21 |     $ref: 'NumericRangeNonNegative#'
22 | 
23 |   latencyDays:
24 |     type: number
25 |     minimum: 1
26 | 
27 |   infectiousPeriodDays:
28 |     type: number
29 |     minimum: 1
30 | 
31 |   hospitalStayDays:
32 |     type: number
33 |     minimum: 1
34 | 
35 |   icuStayDays:
36 |     type: number
37 |     minimum: 1
38 | 
39 |   seasonalForcing:
40 |     type: number
41 |     minimum: 0
42 | 
43 |   peakMonth:
44 |     allOf:
45 |       - $ref: 'IntegerNonNegative#'
46 |       - maximum: 11
47 | 
48 |   overflowSeverity:
49 |     type: number
50 |     minimum: 0
51 | 


--------------------------------------------------------------------------------
/src/constants.ts:
--------------------------------------------------------------------------------
 1 | export const PROJECT_NAME = 'COVID-19 Scenarios' as const
 2 | export const PROJECT_DESCRIPTION = 'Models of COVID-19 outbreak trajectories and hospital demand' as const
 3 | export const COPYRIGHT_YEAR_START = 2020 as const
 4 | export const COMPANY_NAME = 'NeherLab' as const
 5 | 
 6 | export const DEFAULT_SCENARIO_NAME = 'United States of America' as const
 7 | export const DEFAULT_SEVERITY_DISTRIBUTION = 'Adjusted' as const
 8 | export const CUSTOM_COUNTRY_NAME = 'Custom' as const
 9 | export const NONE_COUNTRY_NAME = 'None' as const
10 | 
11 | export const DOMAIN = process.env.DOMAIN ?? ''
12 | export const DOMAIN_STRIPPED = process.env.DOMAIN_STRIPPED ?? ''
13 | export const URL_FAVICON = `${DOMAIN}/favicon.ico`
14 | export const URL_SOCIAL_IMAGE = `${DOMAIN}/social-1200x600.png`
15 | export const URL_MANIFEST_JSON = `${DOMAIN}/manifest.json`
16 | export const SAFARI_PINNED_TAB_COLOR = '#555555' as const
17 | export const MS_TILE_COLOR = '#2b5797' as const
18 | 
19 | export const TWITTER_USERNAME = '@richardneher' as const
20 | 


--------------------------------------------------------------------------------
/src/helpers/types.ts:
--------------------------------------------------------------------------------
 1 | /*
 2 |  * Implements a branded/tagged/nominal type wrapper
 3 |  *
 4 |  * Brands a Base type with a Tag, such that the resulting "tagged" type is only
 5 |  * compatible with the same tagged type.
 6 |  *
 7 |  * Useful for creating type-safe strings, integers etc., when we want to make
 8 |  * sure that a type cannot be accidentally mixed with other similar types.
 9 |  *
10 |  * Example:
11 |  *
12 |  * type UserId = Tagged<string, 'UserId'>
13 |  *
14 |  * let userId = 'user-1' as UserId // cast is important here
15 |  *
16 |  * userId = 'any string' // Error: TS2322: Type '"any string"' is not
17 |  *                       // assignable to type 'Tagged<string, "UserId">'.
18 |  *                       // Type '"any string"' is not assignable to
19 |  *                       // type '{ __tag: "UserId"; }'.
20 |  */
21 | export type Tagged<Base, Tag extends string> = Base & { __tag: Tag }
22 | 
23 | /* Type-safe string. Useful for all kinds of identifiers */
24 | export type Id<Tag extends string> = Tagged<string, Tag>
25 | 


--------------------------------------------------------------------------------
/src/components/Common/ButtonTransparent.tsx:
--------------------------------------------------------------------------------
 1 | import { Button, ButtonProps } from 'reactstrap'
 2 | import styled from 'styled-components'
 3 | 
 4 | export interface ButtonTransparentProps extends ButtonProps {
 5 |   height: string
 6 |   width?: string
 7 |   fontSize: string
 8 | }
 9 | 
10 | export const ButtonTransparent = styled(Button)<ButtonTransparentProps>`
11 |   display: block;
12 |   width: ${(props) => props.width ?? props.height};
13 |   height: ${(props) => props.height};
14 |   line-height: ${(props) => props.height};
15 |   font-size: ${(props) => props.fontSize};
16 |   padding: 0;
17 |   margin: 4px 0;
18 |   background-color: transparent;
19 |   background-image: none;
20 |   color: #cccccc;
21 |   border: none;
22 |   border-radius: 0;
23 |   box-shadow: none;
24 |   border-image: none;
25 |   text-decoration: none;
26 | 
27 |   &:active,
28 |   &:hover,
29 |   &:focus,
30 |   &:focus-within {
31 |     background-color: transparent;
32 |     background-image: none;
33 |     color: #fff;
34 |     text-decoration: none;
35 |   }
36 | `
37 | 


--------------------------------------------------------------------------------
/config/jest/jest.eslint.config.js:
--------------------------------------------------------------------------------
 1 | require('../dotenv')
 2 | 
 3 | const { findModuleRoot } = require('../../lib/findModuleRoot')
 4 | 
 5 | const { moduleRoot } = findModuleRoot()
 6 | 
 7 | module.exports = {
 8 |   rootDir: moduleRoot,
 9 |   roots: ['<rootDir>/src'],
10 |   runner: 'jest-runner-eslint',
11 |   displayName: { name: 'lint', color: 'blue' },
12 |   testEnvironment: 'jest-environment-jsdom',
13 |   preset: 'ts-jest',
14 |   globals: {
15 |     'ts-jest': {
16 |       babelConfig: true,
17 |       diagnostics: {
18 |         pathRegex: /(\/__tests?__\/.*|([./])(test|spec))\.[jt]sx?$/,
19 |         warnOnly: true,
20 |       },
21 |     },
22 |   },
23 |   testMatch: [
24 |     '<rootDir>/src/**/*.(spec|test).{js,jsx,ts,tsx}',
25 |     '<rootDir>/src/**/__test__/**/*.{js,jsx,ts,tsx}',
26 |     '<rootDir>/src/**/__tests__/**/*.{js,jsx,ts,tsx}',
27 |     '<rootDir>/src/**/test/**/*.{js,jsx,ts,tsx}',
28 |     '<rootDir>/src/**/tests/**/*.{js,jsx,ts,tsx}',
29 |   ],
30 |   watchPlugins: [
31 |     'jest-runner-eslint/watch-fix', // prettier-ignore
32 |   ],
33 | }
34 | 


--------------------------------------------------------------------------------
/config/jest/jest.config.js:
--------------------------------------------------------------------------------
 1 | require('../dotenv')
 2 | 
 3 | const path = require('path')
 4 | 
 5 | const { findModuleRoot } = require('../../lib/findModuleRoot')
 6 | 
 7 | const { moduleRoot } = findModuleRoot()
 8 | 
 9 | const shouldRunEslint = process.env.WITH_ESLINT === '1'
10 | 
11 | module.exports = {
12 |   rootDir: moduleRoot,
13 | 
14 |   projects: [require('./jest.tests.config.js'), shouldRunEslint && require('./jest.eslint.config.js')].filter(Boolean),
15 | 
16 |   coverageDirectory: path.join(moduleRoot, '.reports', 'coverage'),
17 | 
18 |   collectCoverageFrom: [
19 |     '!<rootDir>/**/*.d.ts',
20 |     '!<rootDir>/**/node_modules/**/*',
21 |     '<rootDir>/src/**/*.{js,jsx,ts,tsx}',
22 |     '!<rootDir>/src/index.polyfilled.{js,jsx,ts,tsx}',
23 |     '!<rootDir>/src/locales/**/*',
24 |   ],
25 | 
26 |   cacheDirectory: '<rootDir>/.cache/jest',
27 | 
28 |   coverageThreshold: {
29 |     global: {
30 |       // TODO: write more tests?
31 |       // branches: 33,
32 |       // functions: 33,
33 |       // lines: 33,
34 |       // statements: 33,
35 |     },
36 |   },
37 | }
38 | 


--------------------------------------------------------------------------------
/data/hospital-data/hospital_eurostat.tsv:
--------------------------------------------------------------------------------
 1 | country	AcuteCare	AcuteCarPer100k	IMCU	ICU 	CriticalCare	CriticalCarePer100k	percentOfTotal	GDP
 2 | Belgium	56927							
 3 | Bulgaria	43646							
 4 | Czechia	43531							
 5 | Denmark	14621							
 6 | Germany	497182							
 7 | Estonia	4539							
 8 | Ireland	13297							
 9 | Greece	38747							
10 | Spain	113042							
11 | France	206619							
12 | Croatia	14475							
13 | Italy	158891							
14 | Cyprus	2922							
15 | Latvia	6407							
16 | Lithuania	15477							
17 | Luxembourg	2251							
18 | Hungary	41803							
19 | Malta	1486							
20 | Netherlands	50047							
21 | Austria	47920							
22 | Poland	184230							
23 | Portugal	33447							
24 | Romania	102899							
25 | Slovenia	8686							
26 | Slovakia	26692							
27 | Finland	15397							
28 | Sweden	20477							
29 | United Kingdom of Great Britain and Northern Ireland	139647							
30 | Iceland	862							
31 | Liechtenstein	91							
32 | Norway	16885							
33 | Switzerland	30057							
34 | North Macedonia	5937							
35 | Serbia	32585							
36 | Turkey	223386							
37 | 


--------------------------------------------------------------------------------
/data/Makefile:
--------------------------------------------------------------------------------
 1 | 
 2 | .PHONY: all clean data-for-app data-for-app
 3 | 
 4 | all: clean types data-for-app
 5 | 
 6 | clean: clean-types
 7 | 
 8 | clean-types:
 9 | 	rm -rf generated/**
10 | 
11 | types: clean-types
12 | 	cd .. && yarn install && yarn schema:totypes
13 | 
14 | tsv-data:
15 | 	python3 generate_data.py \
16 | 		--fetch
17 | 
18 | recalculated-fits:
19 | 	python3 generate_data.py \
20 | 		--recalculate \
21 | 		--num-threads 10 \
22 | 		--output-scenarios ../src/assets/data/scenarios.json \
23 | 		--output-cases ../src/assets/data/caseCounts.json
24 | 
25 | population:
26 | 	python3 generate_data.py \
27 | 		--output-population populationData.tsv
28 | 
29 | cases:
30 | 	python3 generate_data.py \
31 | 		--output-cases ../src/assets/data/caseCounts.json
32 | 
33 | scenarios:
34 | 	python3 generate_data.py \
35 | 		--output-scenarios ../src/assets/data/scenarios.json
36 | 
37 | test-scenarios:
38 | 	python3 generate_data.py \
39 | 		--output-scenarios test.json
40 | 
41 | test-cases:
42 | 	python3 generate_data.py \
43 | 		--output-cases test.json
44 | 
45 | data-for-app: cases scenarios
46 | 


--------------------------------------------------------------------------------
/src/components/Common/Plausible.tsx:
--------------------------------------------------------------------------------
 1 | /**
 2 |  * Taken with modifications from
 3 |  * https://github.com/4lejandrito/next-plausible/blob/a8e6c2df06b6e8943017d59903ab54e24667ffe2/index.tsx#L1
 4 |  *
 5 |  * By 4lejandrito
 6 |  */
 7 | 
 8 | import React from 'react'
 9 | import Head from 'next/head'
10 | import { get, noop } from 'lodash'
11 | 
12 | export interface PlausibleProps {
13 |   domain: string
14 |   plausibleDomain?: string
15 | }
16 | 
17 | export const PLAUSIBLE_DOMAIN_DEFAULT = 'https://plausible.io'
18 | 
19 | export function Plausible({ domain, plausibleDomain = PLAUSIBLE_DOMAIN_DEFAULT }: PlausibleProps) {
20 |   if (process.env.NODE_ENV !== 'production') {
21 |     return null
22 |   }
23 | 
24 |   const plausibleJs = `${plausibleDomain}/js/plausible.js`
25 | 
26 |   return (
27 |     <Head>
28 |       <script async defer data-domain={domain} src={plausibleJs} />
29 |     </Head>
30 |   )
31 | }
32 | 
33 | export type PlausibleHookResult = (event: string) => void
34 | 
35 | export function usePlausible() {
36 |   return get(window, 'plausible', noop) as PlausibleHookResult
37 | }
38 | 


--------------------------------------------------------------------------------
/src/components/Form/__tests__/FormLabel.test.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | import { render } from '@testing-library/react'
 3 | import FormLabel from '../FormLabel'
 4 | 
 5 | const findLabelInTree = (el: HTMLElement | null): HTMLElement | null => {
 6 |   if (!el) {
 7 |     return null
 8 |   }
 9 |   if ('htmlFor' in el) {
10 |     return el
11 |   }
12 |   return findLabelInTree(el.parentElement)
13 | }
14 | 
15 | describe('FormLabel', () => {
16 |   it('creates a label for an identified form field', () => {
17 |     // A somewhat hacky test - there should be a <label> somewhere in the
18 |     // element tree that shows the label text. And that <label> should be for
19 |     // the identifier.
20 | 
21 |     const { getByText } = render(<FormLabel identifier="abc" label="def" />)
22 | 
23 |     const labelElement = findLabelInTree(getByText('def')) as HTMLLabelElement
24 | 
25 |     expect(labelElement).not.toBeNull()
26 |     if (labelElement) {
27 |       // eslint-disable-next-line jest/no-conditional-expect
28 |       expect(labelElement.htmlFor).toBe('abc')
29 |     }
30 |   })
31 | })
32 | 


--------------------------------------------------------------------------------
/src/types/recharts.d.ts:
--------------------------------------------------------------------------------
 1 | // Temporary fixes for recharts v2.x.x-beta, until the typings are updated
 2 | declare module 'recharts' {
 3 |   export * from '@types/recharts'
 4 | 
 5 |   import { Point } from '@types/recharts'
 6 | 
 7 |   // How do you call payload inside a payload?
 8 |   export interface LegendPayloadPayload {
 9 |     activeDot?: boolean
10 |     animateNewValues?: boolean
11 |     animationBegin?: number
12 |     animationDuration?: number
13 |     animationEasing?: string
14 |     connectNulls?: false
15 |     dataKey?: string
16 |     dot?: false
17 |     fill?: string
18 |     hide?: false
19 |     isAnimationActive?: false
20 |     legendType?: string
21 |     name?: string
22 |     points?: Point[]
23 |     length?: number
24 |     stroke?: string
25 |     strokeWidth?: number
26 |     type?: string
27 |     xAxisId?: number
28 |     yAxisId?: number
29 |   }
30 | 
31 |   export interface LegendPayload {
32 |     color?: string
33 |     dataKey?: string
34 |     inactive?: boolean
35 |     payload?: LegendPayloadPayload
36 |     type: string
37 |     value: string
38 |   }
39 | }
40 | 


--------------------------------------------------------------------------------
/data/hospital-data/ICU_asia.tsv:
--------------------------------------------------------------------------------
 1 | country	AcuteCare	AcuteCarPer100k	IMCU	ICU 	CriticalCare	CriticalCarePer100k	percentOfTotal	GDP
 2 | Bangladesh	32611		296	878	1174	0.7	3.6	
 3 | India	810730			29997	29997	2.3	3.7	
 4 | Indonesia	308435			7094	7094	2.7	2.3	
 5 | Lao People's Democratic Republic				152	152	2.1		
 6 | Mongolia	10840			271	271	8.8	2.5	
 7 | Myanmar	58600		255	331	586	1.1	1	
 8 | Nepal			237	578	815	2.8		
 9 | Pakistan	125680			3142	3142	1.5	2.5	
10 | Philippines	63108			2315	2335	2.2	3.7	
11 | Sri Lanka	86500			519	519	2.3	0.6	
12 | China	5494778			49453	49453	3.6	0.9	
13 | Iran (Islamic Republic of)	130690			3769	3790	4.6	2.9	
14 | Kazakhstan	101231			3948	3948	21.3	3.9	
15 | Malaysia	62353			1060	1060	3.4	1.7	
16 | Thailand	139216			7100	7100	10.4	5.1	
17 | Brunei Darussalam	1234			58	58	13.1	4.7	
18 | Hong Kong	18926			287	511	7.1	2.7	
19 | Japan	710846			5973	9241	7.3	1.3	
20 | Oman	5736			196	499	14.6	8.7	
21 | Saudi Arabia	70815			6515	6515	22.8	9.2	
22 | Singapore	10167			335	671	11.4	6.6	
23 | Korea, Republic of	270100			5402	5402	10.6	2	
24 | Taiwan, Province of China	73637			5758	6701	28.5	9.1	
25 | 


--------------------------------------------------------------------------------
/src/io/serialization/versioning.ts:
--------------------------------------------------------------------------------
 1 | /* eslint-disable camelcase */
 2 | 
 3 | import { last } from 'lodash'
 4 | 
 5 | import semver from 'semver'
 6 | 
 7 | import type { ScenarioParameters } from '../../algorithms/types/Param.types'
 8 | 
 9 | import { getOrThrow } from '../../helpers/getOrThrow'
10 | 
11 | import v2_0_0 from './v2.0.0/serialize'
12 | import v2_1_0 from './v2.1.0/serialize'
13 | import v2_2_0 from './v2.2.0/serialize'
14 | 
15 | export type Serializer = (input: ScenarioParameters) => string
16 | export type Deserializer = (input: string) => ScenarioParameters
17 | 
18 | export interface Serializers {
19 |   serialize: Serializer
20 |   deserialize: Deserializer
21 | }
22 | 
23 | export const SERIALIZERS = new Map<string, Serializers>(
24 |   Object.entries({
25 |     ...v2_0_0,
26 |     ...v2_1_0,
27 |     ...v2_2_0,
28 |   }),
29 | )
30 | 
31 | export const SERIALIZER_VERSIONS = semver.sort(Array.from(SERIALIZERS.keys()))
32 | export const SERIALIZER_VERSION_LATEST = last(SERIALIZER_VERSIONS) ?? 'NO_SERIALIZERS'
33 | export const SERIALIZER_LATEST = getOrThrow(SERIALIZERS, SERIALIZER_VERSION_LATEST)
34 | 


--------------------------------------------------------------------------------
/src/state/sagas.ts:
--------------------------------------------------------------------------------
 1 | import { Saga } from 'redux-saga'
 2 | import { all, call, put } from 'redux-saga/effects'
 3 | 
 4 | import { errorAdd } from './error/error.actions'
 5 | 
 6 | import algorithmSagas from './algorithm/algorithm.sagas'
 7 | import scenarioSagas from './scenario/scenario.sagas'
 8 | import settingsSagas from './settings/settings.sagas'
 9 | import uiSagas from './ui/ui.sagas'
10 | 
11 | export function autoRestart(generator: Saga, handleError: Saga<[Error]>) {
12 |   return function* autoRestarting() {
13 |     while (true) {
14 |       try {
15 |         yield call(generator)
16 |         break
17 |       } catch (error) {
18 |         yield handleError(error)
19 |       }
20 |     }
21 |   }
22 | }
23 | 
24 | export function* rootSaga() {
25 |   yield all([...algorithmSagas, ...scenarioSagas, ...settingsSagas, ...uiSagas])
26 | }
27 | 
28 | export function* rootSagaErrorHandler(error: Error) {
29 |   console.error(error.message)
30 |   console.error(error.stack)
31 |   yield put(errorAdd({ error }))
32 | }
33 | 
34 | export function createRootSaga() {
35 |   return autoRestart(rootSaga, rootSagaErrorHandler)
36 | }
37 | 


--------------------------------------------------------------------------------
/src/styles/font-family-system.scss:
--------------------------------------------------------------------------------
 1 | @font-face {
 2 |   font-family: system-sans;
 3 |   font-style: normal;
 4 |   font-weight: 300;
 5 |   src: local('-apple-system'), local('BlinkMacSystemFont'), local('Segoe UI'), local('Roboto'), local('DroidSans'),
 6 |     local('Oxygen-Sans'), local('Ubuntu'), local('Cantarell'), local('Helvetica Neue'), local('Helvetica'),
 7 |     local('Arial'), local('Tahoma'), local('Noto Sans'), local('sans-serif'), local('Apple Color Emoji'),
 8 |     local('Segoe UI Emoji'), local('Segoe UI Symbol'), local('Noto Color Emoji');
 9 | }
10 | 
11 | @font-face {
12 |   font-family: system-serif;
13 |   font-style: normal;
14 |   font-weight: 300;
15 |   src: local('Times New Roman'), local('Palatino Linotype'), local('Palatino'), local('Georgia'), local('Book Antiqua'),
16 |     local('Times'), local('serif');
17 | }
18 | 
19 | @font-face {
20 |   font-family: system-mono;
21 |   font-style: normal;
22 |   font-weight: 300;
23 |   src: local('SFMono-Regular'), local('Consolas'), local('Liberation Mono'), local('Menlo'), local('Monaco'),
24 |     local('Courier New'), local('Courier'), local('monospace');
25 | }
26 | 


--------------------------------------------------------------------------------
/src/components/Buttons/ClipboardButton.tsx:
--------------------------------------------------------------------------------
 1 | import React, { useState } from 'react'
 2 | 
 3 | import classNames from 'classnames'
 4 | import { useTranslation } from 'react-i18next'
 5 | import { Button, ButtonProps } from 'reactstrap'
 6 | import { MdContentCopy } from 'react-icons/md'
 7 | 
 8 | import { copyToClipboard } from '../../helpers/copyToClipboard'
 9 | 
10 | interface ClipboardButtonProps extends ButtonProps {
11 |   textToCopy?: string
12 | }
13 | 
14 | /**
15 |  * When clicked, copies textToCopy to clipboard
16 |  */
17 | export function ClipboardButton({ textToCopy, className, ...restProps }: ClipboardButtonProps) {
18 |   const { t } = useTranslation()
19 |   const [isCopied, setIsCopied] = useState(false)
20 |   const onClick = () => {
21 |     if (textToCopy) {
22 |       copyToClipboard(String(textToCopy))
23 |       setIsCopied(true)
24 |     }
25 |   }
26 | 
27 |   return (
28 |     <Button className={classNames(className, 'clipboard-button')} onClick={onClick} {...restProps}>
29 |       <MdContentCopy />
30 |       <span className="ml-1">{isCopied ? t('Copied!') : t('Copy link')}</span>
31 |     </Button>
32 |   )
33 | }
34 | 


--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
 1 | MIT License
 2 | 
 3 | Copyright (c) 2020 neherlab
 4 | 
 5 | Permission is hereby granted, free of charge, to any person obtaining a copy
 6 | of this software and associated documentation files (the "Software"), to deal
 7 | in the Software without restriction, including without limitation the rights
 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 | 
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 | 
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 | 


--------------------------------------------------------------------------------
/data/scripts/mapping.py:
--------------------------------------------------------------------------------
 1 | import numpy as np
 2 | R0s_mapping = R0s = np.linspace(0.2,10,100)
 3 | GR_mapping = [-0.17576, -0.15435, -0.12755, -0.10184, -0.07822, -0.05661, -0.03675, -0.01837,
 4 |  -0.00126,  0.01477,  0.02987,  0.04414,  0.05769,  0.0706,   0.08293,  0.09474,
 5 |   0.10609,  0.117,    0.12753,  0.13769,  0.14752,  0.15705,  0.16628,  0.17526,
 6 |   0.18398,  0.19247,  0.20074,  0.2088,   0.21667,  0.22436,  0.23187,  0.23922,
 7 |   0.2464,   0.25345,  0.26034,  0.26711,  0.27374,  0.28025,  0.28664,  0.29292,
 8 |   0.29909,  0.30516,  0.31112,  0.31699,  0.32277,  0.32845,  0.33405,  0.33957,
 9 |   0.345,    0.35036,  0.35564,  0.36085,  0.36599,  0.37106,  0.37606,  0.38101,
10 |   0.38588,  0.3907,  0.39546,  0.40016,  0.4048,  0.4094,  0.41393,  0.41842,
11 |   0.42286,  0.42725,  0.43159,  0.43588,  0.44013,  0.44434,  0.4485,  0.45262,
12 |   0.45669,  0.46073,  0.46473,  0.46869,  0.47261,  0.47649,  0.48034,  0.48415,
13 |   0.48792,  0.49167,  0.49537,  0.49905,  0.50269,  0.50629,  0.50987,  0.51341,
14 |   0.51692,  0.52041,  0.52386,  0.52728,  0.53067,  0.53403,  0.53736,  0.54066,
15 |   0.54393,  0.54718,  0.55039,  0.55357,]
16 | 


--------------------------------------------------------------------------------
/src/components/Main/Results/PlotSpinner.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import Loader from 'react-loader-spinner'
 4 | import { connect } from 'react-redux'
 5 | 
 6 | import { selectIsRunning } from '../../../state/algorithm/algorithm.selectors'
 7 | import { State } from '../../../state/reducer'
 8 | 
 9 | export interface RunningSpinerProps {
10 |   size: number
11 | }
12 | 
13 | export function RunningSpinner({ size }: RunningSpinerProps) {
14 |   return <Loader type="ThreeDots" color="#495057" height={size} width={size} />
15 | }
16 | 
17 | export interface PlotSpinnerProps {
18 |   isRunning: boolean
19 |   size: number
20 | }
21 | 
22 | const mapStateToProps = (state: State) => ({
23 |   isRunning: selectIsRunning(state),
24 | })
25 | 
26 | const mapDispatchToProps = {}
27 | 
28 | export const PlotSpinner = connect(mapStateToProps, mapDispatchToProps)(PlotSpinnerDisconnected)
29 | 
30 | export function PlotSpinnerDisconnected({ isRunning, size = 75 }: PlotSpinnerProps) {
31 |   if (!isRunning) {
32 |     return null
33 |   }
34 | 
35 |   return (
36 |     <div className="spinner-container">
37 |       <RunningSpinner size={size} />
38 |     </div>
39 |   )
40 | }
41 | 


--------------------------------------------------------------------------------
/src/state/settings/settings.selectors.ts:
--------------------------------------------------------------------------------
 1 | import type { State } from '../reducer'
 2 | import { LocaleKey, LocaleWithKey, getLocaleWithKey } from '../../i18n/i18n'
 3 | 
 4 | export const selectIsAutorunEnabled = (state: State): boolean => state.settings.isAutorunEnabled
 5 | 
 6 | export const selectIsLogScale = (state: State): boolean => state.settings.isLogScale
 7 | 
 8 | export const selectShouldFormatNumbers = (state: State): boolean => state.settings.shouldFormatNumbers
 9 | 
10 | export const selectShouldShowPlotLabels = (state: State): boolean => state.settings.selectShouldShowPlotLabels
11 | 
12 | export const selectAreResultsMaximized = (state: State): boolean => state.settings.areResultsMaximized
13 | 
14 | export const selectDisclaimerVersionAccepted = (state: State): number | undefined =>
15 |   state.settings.disclaimerVersionAccepted
16 | 
17 | export const selectDisclaimerShouldSuppress = (state: State): boolean => state.settings.disclaimerShouldSuppress
18 | 
19 | export const selectLocaleKey = (state: State): LocaleKey => state.settings.localeKey
20 | 
21 | export const selectLocale = (state: State): LocaleWithKey => getLocaleWithKey(selectLocaleKey(state))
22 | 


--------------------------------------------------------------------------------
/data/case-counts/india/IND-Dadar Nagar Haveli.tsv:
--------------------------------------------------------------------------------
 1 | # Data source: https://api.rootnet.in/covid19-in/stats/daily
 2 | # Data provenance: https://github.com/amodm/api-covid19-in
 3 | # License: Scraped from Ministry of Health and Family Welfare plus other sources, no clear license
 4 | time	cases	deaths	hospitalized	icu	recovered
 5 | 2020-05-06	1	0			
 6 | 2020-05-07	1	0			
 7 | 2020-05-08	1	0			
 8 | 2020-05-09	1	0			
 9 | 2020-05-10	1	0			
10 | 2020-05-11	1	0			
11 | 2020-05-12	1	0			
12 | 2020-05-13	1	0			
13 | 2020-05-14	1	0			
14 | 2020-05-15	1	0			
15 | 2020-05-16	1	0			
16 | 2020-05-17	1	0			
17 | 2020-05-18	1	0			
18 | 2020-05-19	1	0			
19 | 2020-05-20	1	0			
20 | 2020-05-21	1	0			
21 | 2020-05-22	1	0			
22 | 2020-05-23	1	0			
23 | 2020-05-24	2	0			
24 | 2020-05-25	2	0			
25 | 2020-05-26	2	0			
26 | 2020-05-27	2	0			
27 | 2020-05-28	2	0			
28 | 2020-05-29	2	0			
29 | 2020-05-30	2	0			
30 | 2020-05-31	2	0			
31 | 2020-06-01	2	0			
32 | 2020-06-02	3	0			
33 | 2020-06-03	4	0			
34 | 2020-06-04	8	0			
35 | 2020-06-05	12	0			
36 | 2020-06-06	14	0			
37 | 2020-06-07	19	0			
38 | 2020-06-08	20	0			
39 | 2020-06-09	22	0			
40 | 2020-06-10	22	0			
41 | 


--------------------------------------------------------------------------------
/src/algorithms/types/convert.ts:
--------------------------------------------------------------------------------
 1 | import { omit } from 'lodash'
 2 | 
 3 | import { uuidv4 } from '../../helpers/uuid'
 4 | 
 5 | import { MitigationInterval, MitigationIntervalExternal, ScenarioDatum, ScenarioDatumExternal } from './Param.types'
 6 | 
 7 | export function addId(interval: MitigationIntervalExternal): MitigationInterval {
 8 |   return { ...interval, id: uuidv4() }
 9 | }
10 | 
11 | export function removeId(interval: MitigationInterval): MitigationIntervalExternal {
12 |   return omit(interval, 'id')
13 | }
14 | 
15 | export function toInternal(scenario: ScenarioDatumExternal): ScenarioDatum {
16 |   const { mitigationIntervals } = scenario.mitigation
17 |   return {
18 |     ...scenario,
19 |     mitigation: {
20 |       ...scenario.mitigation,
21 |       mitigationIntervals: mitigationIntervals.map(addId),
22 |     },
23 |   }
24 | }
25 | 
26 | export function toExternal(scenario: ScenarioDatum): ScenarioDatumExternal {
27 |   const { mitigationIntervals } = scenario.mitigation
28 |   return {
29 |     ...scenario,
30 |     mitigation: {
31 |       ...scenario.mitigation,
32 |       mitigationIntervals: mitigationIntervals.map(removeId),
33 |     },
34 |   }
35 | }
36 | 


--------------------------------------------------------------------------------
/src/components/Main/ScenarioLoader/__tests__/ScenarioLoader.test.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import { cleanup, fireEvent, RenderResult } from '@testing-library/react'
 4 | 
 5 | import { render } from 'src/helpers/testReactRedux'
 6 | 
 7 | import { ScenarioLoader } from '../ScenarioLoader'
 8 | 
 9 | describe('ScenarioLoader', () => {
10 |   let scenarioLoader: RenderResult
11 |   let onClose: () => void
12 | 
13 |   let useDebounceMock: typeof jest
14 | 
15 |   beforeAll(() => {
16 |     useDebounceMock = jest.mock('use-debounce', () => ({
17 |       useDebouncedCallback: (f: () => unknown) => f,
18 |     }))
19 |   })
20 | 
21 |   afterAll(async () => {
22 |     useDebounceMock.clearAllMocks()
23 |     cleanup()
24 |   })
25 | 
26 |   beforeEach(() => {
27 |     onClose = jest.fn()
28 |     scenarioLoader = render(<ScenarioLoader />)
29 |   })
30 | 
31 |   it('renders a header', () => {
32 |     expect(scenarioLoader.getByText('Change scenario')).not.toBeNull()
33 |   })
34 | 
35 |   it('closes', () => {
36 |     const closeButton = scenarioLoader.getByLabelText('Close')
37 |     fireEvent.click(closeButton)
38 |     expect(onClose).toHaveBeenCalled()
39 |   })
40 | })
41 | 


--------------------------------------------------------------------------------
/src/components/Faq/FaqTableOfContents.tsx:
--------------------------------------------------------------------------------
 1 | /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 2 | import React, { useState, useEffect } from 'react'
 3 | 
 4 | import { get } from 'lodash'
 5 | 
 6 | // FIXME: this has t be refactored. Remove DOM manipulation,
 7 | //  reliance on HTML content, forEach() should be a map
 8 | const FaqTableOfContents = () => {
 9 |   const [content, setContent] = useState<string[]>([])
10 |   useEffect(() => {
11 |     const links: string[] = []
12 |     setTimeout(() => {
13 |       Array.from(document.querySelectorAll('strong')).forEach((node) => {
14 |         if (node.innerHTML === 'Q:') {
15 |           node.id = `q${links.length}`
16 |           const textContent = get(node, 'parentNode.lastChild.textContent')
17 |           if (textContent) {
18 |             links.push(textContent)
19 |           }
20 |         }
21 |       })
22 |       setContent(links)
23 |     }, 0)
24 |   }, [])
25 |   return (
26 |     <ol>
27 |       {content.map((question, idx) => (
28 |         <li key={question}>
29 |           <a href={`#q${idx}`}>{question}</a>
30 |         </li>
31 |       ))}
32 |     </ol>
33 |   )
34 | }
35 | 
36 | export default FaqTableOfContents
37 | 


--------------------------------------------------------------------------------
/data/scripts/transform_ages.py:
--------------------------------------------------------------------------------
 1 | import os
 2 | import sys
 3 | sys.path.append('..')
 4 | 
 5 | import json
 6 | import argparse
 7 | 
 8 | # -----------------------------------------------------------------------
 9 | # Globals
10 | 
11 | def flatten(db):
12 |     entries = []
13 |     for country, ages in db.items():
14 |         entry = {"country" : country, "ageDistribution": ages}
15 |         entries.append(entry)
16 | 
17 |     return entries
18 | 
19 | # -----------------------------------------------------------------------
20 | # Main point of entry
21 | 
22 | parser = argparse.ArgumentParser(description="Transforms age distribution JSON into list of entries")
23 | parser.add_argument('--input', type=str, help="path to input age distribution json to transform")
24 | parser.add_argument('--output', type=str, help="path to output transformed age distribution json")
25 | 
26 | args = parser.parse_args()
27 | if __name__ == "__main__":
28 |     if not os.path.exists(args.input):
29 |         print(f"Error: '{args.input}' not a valid path")
30 | 
31 |     old_json = json.load(open(args.input))
32 |     new_json = flatten(old_json)
33 |     with open(args.output, 'w+') as out:
34 |         json.dump(new_json, out)
35 | 


--------------------------------------------------------------------------------
/src/io/defaults/getScenarioData.ts:
--------------------------------------------------------------------------------
 1 | import validateScenarioArray, { errors } from '../../.generated/latest/validateScenarioArray'
 2 | 
 3 | import type { ScenarioArray, ScenarioData } from '../../algorithms/types/Param.types'
 4 | 
 5 | import { Convert } from '../../algorithms/types/Param.types'
 6 | 
 7 | import scenariosRaw from '../../assets/data/scenarios.json'
 8 | 
 9 | import { toInternal } from '../../algorithms/types/convert'
10 | 
11 | function validate() {
12 |   const valid = validateScenarioArray(scenariosRaw)
13 |   if (!valid) {
14 |     throw errors
15 |   }
16 | 
17 |   return ((scenariosRaw as unknown) as ScenarioArray).all
18 | }
19 | 
20 | const scenarios = validate()
21 | export const scenarioNames = scenarios.map((scenario) => scenario.name)
22 | 
23 | export function getScenarioData(name: string): ScenarioData {
24 |   const scenarioFound = scenarios.find((s) => s.name === name)
25 |   if (!scenarioFound) {
26 |     throw new Error(`Error: scenario "${name}" not found in JSON`)
27 |   }
28 | 
29 |   // FIXME: this should be changed, too hacky
30 |   const scenarioData = Convert.toScenarioData(JSON.stringify(scenarioFound))
31 |   return { ...scenarioData, data: toInternal(scenarioData.data) }
32 | }
33 | 


--------------------------------------------------------------------------------
/data/case-counts/owid/Niue.tsv:
--------------------------------------------------------------------------------
 1 | # Data source: https://covid.ourworldindata.org/data/owid-covid-data.json
 2 | # Data provenance: Our World in Data
 3 | # License: CC-BY
 4 | time	cases	deaths	hospitalized	icu	recovered
 5 | 2021-06-21	0	0			
 6 | 2021-06-22	0	0			
 7 | 2021-06-23	0	0			
 8 | 2021-06-24	0	0			
 9 | 2021-06-25	0	0			
10 | 2021-06-26	0	0			
11 | 2021-06-27	0	0			
12 | 2021-06-28	0	0			
13 | 2021-06-29	0	0			
14 | 2021-06-30	0	0			
15 | 2021-07-01	0	0			
16 | 2021-07-02	0	0			
17 | 2021-07-03	0	0			
18 | 2021-07-04	0	0			
19 | 2021-07-05	0	0			
20 | 2021-07-06	0	0			
21 | 2021-07-07	0	0			
22 | 2021-07-08	0	0			
23 | 2021-07-09	0	0			
24 | 2021-07-10	0	0			
25 | 2021-07-11	0	0			
26 | 2021-07-12	0	0			
27 | 2021-07-13	0	0			
28 | 2021-07-14	0	0			
29 | 2021-07-15	0	0			
30 | 2021-07-16	0	0			
31 | 2021-07-17	0	0			
32 | 2021-07-18	0	0			
33 | 2021-07-19	0	0			
34 | 2021-07-20	0	0			
35 | 2021-07-21	0	0			
36 | 2021-07-22	0	0			
37 | 2021-07-23	0	0			
38 | 2021-07-24	0	0			
39 | 2021-07-25	0	0			
40 | 2021-07-26	0	0			
41 | 2021-07-27	0	0			
42 | 2021-07-28	0	0			
43 | 2021-07-29	0	0			
44 | 2021-07-30	0	0			
45 | 2021-07-31	0	0			
46 | 2021-08-01	0	0			
47 | 2021-08-02	0	0			
48 | 


--------------------------------------------------------------------------------
/src/components/Main/Controls/UrlTextInput.tsx:
--------------------------------------------------------------------------------
 1 | import React, { useRef } from 'react'
 2 | 
 3 | import classNames from 'classnames'
 4 | import { Input, InputProps } from 'reactstrap'
 5 | 
 6 | export interface UrlTextInputProps extends InputProps {
 7 |   text: string
 8 | }
 9 | 
10 | function UrlTextInput({ text, className, ...restProps }: UrlTextInputProps) {
11 |   const inputRef = useRef<HTMLInputElement>()
12 | 
13 |   function selectAll() {
14 |     const input = inputRef?.current
15 |     if (!input) {
16 |       return
17 |     }
18 |     input.select()
19 |   }
20 | 
21 |   return (
22 |     <Input
23 |       className={classNames('form-control', 'url-text-input', 'h-100', className)}
24 |       type="text"
25 |       value={text}
26 |       onFocus={selectAll}
27 |       onDoubleClick={selectAll}
28 |       onClick={selectAll}
29 |       // NOTE: This is a bug in @types/reactstrap typings:
30 |       // it claims that `innerRef` is `React.Ref` while in reality it is `React.RefObject`
31 |       // eslint-disable-next-line @typescript-eslint/ban-ts-comment
32 |       // @ts-ignore
33 |       innerRef={inputRef}
34 |       readOnly
35 |       {...restProps}
36 |     />
37 |   )
38 | }
39 | 
40 | export { UrlTextInput }
41 | 


--------------------------------------------------------------------------------
/src/io/serialization/deserialize.ts:
--------------------------------------------------------------------------------
 1 | import semver from 'semver'
 2 | 
 3 | import type { ScenarioParameters } from '../../algorithms/types/Param.types'
 4 | 
 5 | import {
 6 |   DeserializationErrorJsonSyntaxInvalid,
 7 |   DeserializationErrorSchemaVersionInvalid,
 8 |   DeserializationErrorSchemaVersionMissing,
 9 | } from './errors'
10 | 
11 | import { SERIALIZER_VERSIONS, SERIALIZERS } from './versioning'
12 | 
13 | export function deserialize(dataString: string): ScenarioParameters {
14 |   try {
15 |     const shareableDangerous = JSON.parse(dataString) as { schemaVer?: string }
16 | 
17 |     const schemaVer = semver.valid(shareableDangerous?.schemaVer)
18 | 
19 |     if (schemaVer) {
20 |       const deserialize = SERIALIZERS.get(schemaVer)?.deserialize
21 |       if (deserialize) {
22 |         return deserialize(dataString)
23 |       }
24 | 
25 |       throw new DeserializationErrorSchemaVersionInvalid(schemaVer, SERIALIZER_VERSIONS)
26 |     }
27 | 
28 |     throw new DeserializationErrorSchemaVersionMissing()
29 |   } catch (error) {
30 |     if (error instanceof SyntaxError) {
31 |       throw new DeserializationErrorJsonSyntaxInvalid(error.message)
32 |     } else {
33 |       throw error
34 |     }
35 |   }
36 | }
37 | 


--------------------------------------------------------------------------------
/.snyk:
--------------------------------------------------------------------------------
 1 | # Snyk (https://snyk.io) policy file, patches or ignores known vulnerabilities.
 2 | version: v1.14.1
 3 | ignore: {}
 4 | # patches apply the minimum changes required to fix a vulnerability
 5 | patch:
 6 |   SNYK-JS-LODASH-567746:
 7 |     - lodash:
 8 |         patched: '2020-05-02T19:06:59.828Z'
 9 |     - formik > lodash:
10 |         patched: '2020-05-02T19:06:59.828Z'
11 |     - react-dates > lodash:
12 |         patched: '2020-05-02T19:06:59.828Z'
13 |     - react-resize-detector > lodash:
14 |         patched: '2020-05-02T19:06:59.828Z'
15 |     - recharts > lodash:
16 |         patched: '2020-05-02T19:06:59.828Z'
17 |     - yup > lodash:
18 |         patched: '2020-05-02T19:06:59.828Z'
19 |     - recharts > react-resize-detector > lodash:
20 |         patched: '2020-05-02T19:06:59.828Z'
21 |     - recharts > react-smooth > lodash:
22 |         patched: '2020-05-02T19:06:59.828Z'
23 |     - react-select > @emotion/css > babel-plugin-emotion > @babel/helper-module-imports > @babel/types > lodash:
24 |         patched: '2020-05-02T19:06:59.828Z'
25 |     - react-select > @emotion/core > @emotion/css > babel-plugin-emotion > @babel/helper-module-imports > @babel/types > lodash:
26 |         patched: '2020-05-02T19:06:59.828Z'
27 | 


--------------------------------------------------------------------------------
/CONTRIBUTING.md:
--------------------------------------------------------------------------------
 1 | # Contributing
 2 | 
 3 | Thanks for taking the time to contribute. You can ask questions and discuss with other "COVID-19 scenarios" community
 4 | members over the Spectrum chat:
 5 | 
 6 | <p align="center">
 7 |   <a href="https://spectrum.chat/covid19-scenarios/general/questions-discussions~8d49f461-a890-4beb-84f7-2d6ed0ae503a">
 8 |     <img alt="Join the community on Spectrum" src="https://withspectrum.github.io/badge/badge.svg" />
 9 |   </a>
10 | </p>
11 | 
12 | ## Code of Conduct
13 | 
14 | This project and everyone participating in it is governed by the [Code of Conduct](CODE_OF_CONDUCT.md). By
15 | participating, you are expected to uphold this code. Unacceptable behavior won't be tolerated.
16 | 
17 | ## Reporting Bugs
18 | 
19 | When you are creating a bug report, please include as many details as possible. Fill out
20 | [the required template](https://github.com/neherlab/covid19_scenarios/blob/master/.github/ISSUE_TEMPLATE/bug_report.md),
21 | the information it asks for helps us resolve issues faster.
22 | 
23 | ## Acknowledging contributions
24 | 
25 | You can add yourself or others to the table of contributors by follwing the [all-contributors bot usage instructions](https://allcontributors.org/docs/en/bot/usage)
26 | 


--------------------------------------------------------------------------------
/src/workers/algorithm/index.ts:
--------------------------------------------------------------------------------
 1 | import { AlgorithmResult } from '../../algorithms/types/Result.types'
 2 | import { MessageData } from './worker.types'
 3 | 
 4 | import { RunParams } from '../../algorithms/run'
 5 | 
 6 | let runImpl = async (args: RunParams): Promise<AlgorithmResult> => {
 7 |   return Promise.reject(new Error('Web workers are not supported'))
 8 | }
 9 | 
10 | if (typeof Worker !== 'undefined') {
11 |   const worker = new Worker('./worker.ts', { type: 'module', name: 'algorithm' })
12 | 
13 |   runImpl = async (args: RunParams) => {
14 |     return new Promise<AlgorithmResult>((resolve, reject) => {
15 |       worker.addEventListener('message', (message: MessageEvent) => {
16 |         const { result, error }: MessageData = message.data as { result: AlgorithmResult; error: string }
17 | 
18 |         if (result) {
19 |           resolve(result)
20 |           return
21 |         }
22 | 
23 |         if (error) {
24 |           reject(error)
25 |         }
26 |       })
27 | 
28 |       worker.addEventListener('error', (error) => {
29 |         reject(error)
30 |       })
31 | 
32 |       worker.postMessage(args)
33 |     })
34 |   }
35 | }
36 | 
37 | export async function run(args: RunParams) {
38 |   return runImpl(args)
39 | }
40 | 


--------------------------------------------------------------------------------
/src/components/Team/TeamPage.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import { Container, Col, Row } from 'reactstrap'
 4 | import { useTranslation } from 'react-i18next'
 5 | 
 6 | import CoreTeam from './CoreTeam.mdx'
 7 | import ContributorsGenerated from './ContributorsGenerated.mdx'
 8 | 
 9 | export function TeamPage() {
10 |   const { t } = useTranslation()
11 | 
12 |   return (
13 |     <Container>
14 |       <Row>
15 |         <Col>
16 |           <h1>{t('Team')}</h1>
17 | 
18 |           <h2>{t('Initial development')}</h2>
19 |           <CoreTeam />
20 | 
21 |           <h2>{t('Contributors')}</h2>
22 |           <ContributorsGenerated />
23 | 
24 |           <h2>{t('Support')}</h2>
25 | 
26 |           <p>{t('We want to thank the companies that reached out and helped us to build this tool:')}</p>
27 | 
28 |           <p>
29 |             {t(`Vercel (previously known as ZEIT) sponsored to build and host all of your pull requests on their now.sh platform.
30 |              This has helped us enormously, especially when working with external collaborators`)}
31 |           </p>
32 | 
33 |           <p>{t('Github kindly allowed us to use their new Discussions feature')}</p>
34 |         </Col>
35 |       </Row>
36 |     </Container>
37 |   )
38 | }
39 | 


--------------------------------------------------------------------------------
/.travis.yml:
--------------------------------------------------------------------------------
 1 | version: ~> 1.0
 2 | 
 3 | os: linux
 4 | dist: bionic
 5 | 
 6 | branches:
 7 |   only:
 8 |     - master
 9 |     - staging
10 |     - release
11 | 
12 | language: node_js
13 | 
14 | cache: false
15 | 
16 | install:
17 |   - yarn install --frozen-lockfile
18 | 
19 | before_script:
20 |   - cp .env.example .env
21 | 
22 | script:
23 |   - yarn schema:totypes
24 |   - yarn eslint --max-warnings=0
25 | 
26 | before_deploy:
27 |   - yarn prod:build
28 | 
29 | deploy:
30 |   - provider: s3
31 |     edge: true
32 |     detect_encoding: false
33 |     dot_match: true
34 |     local_dir: .build/production/web
35 |     region: $AWS_DEFAULT_REGION
36 |     access_key_id: $AWS_ACCESS_KEY_ID
37 |     secret_access_key: $AWS_SECRET_ACCESS_KEY
38 |     bucket: $AWS_S3_BUCKET
39 |     on:
40 |       all_branches: true
41 |       condition: $TRAVIS_BRANCH =~ ^(master|staging|release)$
42 | 
43 | after_deploy:
44 |   - yarn global add travis-ci-cloudfront-invalidation@1.1.0
45 |   - >
46 |     travis-ci-cloudfront-invalidation \
47 |       -b $TRAVIS_BRANCH -p $TRAVIS_PULL_REQUEST \
48 |       -a $AWS_ACCESS_KEY_ID \
49 |       -s $AWS_SECRET_ACCESS_KEY \
50 |       -c $AWS_CLOUDFRONT_DISTRIBUTION_ID \
51 |       -i '/*' \
52 |       -o 'master,staging,release'
53 | 


--------------------------------------------------------------------------------
/data/parsers/israel.py:
--------------------------------------------------------------------------------
 1 | import sys
 2 | import requests
 3 | import csv
 4 | import io
 5 | from datetime import datetime
 6 | 
 7 | from .utils import store_data, stoi
 8 | 
 9 | # ------------------------------------------------------------------------
10 | # Globals
11 | 
12 | URL  = "https://raw.githubusercontent.com/idandrd/israel-covid19-data/master/IsraelCOVID19.csv"
13 | cols = ['time', 'cases', 'deaths', 'hospitalized', 'icu', 'recovered']
14 | 
15 | # ------------------------------------------------------------------------
16 | # Main point of entry
17 | 
18 | def parse():
19 |     r  = requests.get(URL)
20 |     if not r.ok:
21 |         print(f"Failed to fetch {URL}", file=sys.stderr)
22 |         exit(1)
23 |         r.close()
24 |     il_data = dict(Israel=[])
25 |     fd  = io.StringIO(r.text)
26 |     rdr = csv.reader(fd)
27 |     hdr = next(rdr)
28 |     for row in rdr:
29 |         if len(row[0])==0:
30 |             continue
31 |         date_str = datetime.strptime(row[0], r"%d/%m/%Y").strftime(r"%Y-%m-%d")
32 |         num_cases = stoi(row[1])
33 |         num_icus = stoi(row[4])
34 |         num_deaths = stoi(row[5])
35 |         il_data["Israel"].append([date_str, num_cases, num_deaths, None, num_icus, None])
36 | 
37 |     store_data(il_data, 'israel', cols)
38 | 


--------------------------------------------------------------------------------
/src/io/serialization/serialize.ts:
--------------------------------------------------------------------------------
 1 | import semver from 'semver'
 2 | 
 3 | import type { ScenarioParameters } from '../../algorithms/types/Param.types'
 4 | 
 5 | import { DeserializationErrorSchemaVersionInvalid, SerializationErrorSchemaVersionNotLatest } from './errors'
 6 | 
 7 | import { deserialize } from './deserialize'
 8 | 
 9 | import { SERIALIZER_LATEST, SERIALIZER_VERSION_LATEST, SERIALIZER_VERSIONS } from './versioning'
10 | 
11 | export function serialize(data: ScenarioParameters): string {
12 |   const serializerLatest = SERIALIZER_LATEST.serialize
13 |   const serialized = serializerLatest(data)
14 | 
15 |   // This will verify the quility of serialization in dev mode
16 |   if (process.env.NODE_ENV !== 'production') {
17 |     const shareableDangerous = JSON.parse(serialized) as { schemaVer?: string }
18 |     const schemaVer = semver.valid(shareableDangerous?.schemaVer)
19 | 
20 |     if (schemaVer) {
21 |       if (schemaVer !== SERIALIZER_VERSION_LATEST) {
22 |         throw new SerializationErrorSchemaVersionNotLatest(schemaVer, SERIALIZER_VERSIONS)
23 |       }
24 | 
25 |       deserialize(serialized)
26 |     } else {
27 |       throw new DeserializationErrorSchemaVersionInvalid('Not provided', SERIALIZER_VERSIONS)
28 |     }
29 |   }
30 | 
31 |   return serialized
32 | }
33 | 


--------------------------------------------------------------------------------
/src/styles/components/SeverityTable.scss:
--------------------------------------------------------------------------------
 1 | @import '../variables';
 2 | @import '../mixins';
 3 | 
 4 | .age-group-parameters {
 5 |   // 700 = the point at which the titles break for english
 6 |   // !important because react-grid assigns a width to the table element
 7 |   table {
 8 |     min-width: 700px !important;
 9 |   }
10 | 
11 |   td,
12 |   th {
13 |     padding: 0;
14 |   }
15 | 
16 |   td > input {
17 |     // otherwise bootstrap makes it too large
18 |     height: auto;
19 |     padding: 0;
20 |   }
21 | 
22 |   .dx-g-bs4-table-edit-cell {
23 |     padding: 0 !important;
24 |   }
25 | 
26 |   td p {
27 |     margin: 0;
28 |   }
29 | 
30 |   colgroup col:nth-child(3) {
31 |     background-color: #fdbf6f55;
32 |   }
33 | 
34 |   colgroup col:nth-child(4) {
35 |     background-color: #fb9a9955;
36 |   }
37 | 
38 |   colgroup col:nth-child(5) {
39 |     background-color: #db3c3f55;
40 |   }
41 | 
42 |   colgroup col:nth-child(6) {
43 |     background-color: #e31a1c55;
44 |   }
45 | 
46 |   colgroup col:nth-child(7) {
47 |     background-color: #cab2d655;
48 |   }
49 | 
50 |   colgroup col:nth-child(8) {
51 |     background-color: #a6cee355;
52 |   }
53 | }
54 | 
55 | .age-group-parameters .table-responsive.dx-g-bs4-table-container {
56 |   @include horizontal-scroll-shadow();
57 | }
58 | 


--------------------------------------------------------------------------------
/data/case-counts/china/CHN-Ningxia.tsv:
--------------------------------------------------------------------------------
 1 | # Data source: https://github.com/BlankerL/DXY-COVID-19-Data/raw/master/csv/DXYOverall.csv
 2 | # Data provenance: https://github.com/BlankerL/DXY-COVID-19-Data
 3 | # License: MIT
 4 | time	cases	deaths	hospitalized	icu	recovered
 5 | 2020-01-22	1	0			0
 6 | 2020-01-24	1	0			0
 7 | 2020-01-25	3	0			0
 8 | 2020-01-26	4	0			0
 9 | 2020-01-27	7	0			0
10 | 2020-01-28	11	0			0
11 | 2020-01-29	12	0			0
12 | 2020-01-30	17	0			0
13 | 2020-01-31	21	0			0
14 | 2020-02-01	26	0			0
15 | 2020-02-02	28	0			0
16 | 2020-02-03	31	0			1
17 | 2020-02-04	34	0			1
18 | 2020-02-06	40	0			1
19 | 2020-02-07	43	0			5
20 | 2020-02-08	45	0			15
21 | 2020-02-09	45	0			13
22 | 2020-02-10	49	0			13
23 | 2020-02-11	53	0			22
24 | 2020-02-12	58	0			24
25 | 2020-02-13	64	0			24
26 | 2020-02-14	67	0			24
27 | 2020-02-15	70	0			33
28 | 2020-02-17	70	0			33
29 | 2020-02-18	70	0			42
30 | 2020-02-19	71	0			42
31 | 2020-02-20	71	0			44
32 | 2020-02-21	71	0			48
33 | 2020-02-23	71	0			56
34 | 2020-02-24	71	0			58
35 | 2020-02-25	71	0			61
36 | 2020-02-26	71	0			65
37 | 2020-02-27	72	0			68
38 | 2020-02-29	73	0			69
39 | 2020-03-02	74	0			69
40 | 2020-03-04	75	0			69
41 | 2020-03-06	75	0			71
42 | 2020-03-11	75	0			72
43 | 2020-03-14	75	0			73
44 | 2020-03-16	75	0			75
45 | 


--------------------------------------------------------------------------------
/data/scripts/transform_ages_v2.py:
--------------------------------------------------------------------------------
 1 | import os
 2 | import sys
 3 | sys.path.append('..')
 4 | 
 5 | import json
 6 | import argparse
 7 | 
 8 | # -----------------------------------------------------------------------
 9 | # Functions
10 | 
11 | def expand(data):
12 |     result = []
13 |     for datum in data:
14 |         name = datum["country"]
15 |         elem = [ {"ageGroup" : key, "population" : val} for key, val in datum["ageDistribution"].items() ]
16 |         result.append({"data" : elem, "name" : name})
17 | 
18 |     return { 'all' : result }
19 | 
20 | # -----------------------------------------------------------------------
21 | # Main point of entry
22 | 
23 | parser = argparse.ArgumentParser(description="Transforms age distribution JSON into list of entries")
24 | parser.add_argument('--input', type=str, help="path to input age distribution json to transform")
25 | parser.add_argument('--output', type=str, help="path to output transformed age distribution json")
26 | 
27 | args = parser.parse_args()
28 | if __name__ == "__main__":
29 |     if not os.path.exists(args.input):
30 |         print(f"Error: '{args.input}' not a valid path")
31 | 
32 |     old_json = json.load(open(args.input))
33 |     new_json = expand(old_json)
34 |     with open(args.output, 'w+') as out:
35 |         json.dump(new_json, out)
36 | 


--------------------------------------------------------------------------------
/src/components/Main/Scenario/ScenarioCardContainment.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import { FormikErrors, FormikTouched, FormikValues } from 'formik'
 4 | 
 5 | import { useTranslation } from 'react-i18next'
 6 | 
 7 | import { CollapsibleCard } from '../../Form/CollapsibleCard'
 8 | import { MitigationTable } from '../Mitigation/MitigationTable'
 9 | 
10 | export interface ScenarioCardContainmentProps {
11 |   errors?: FormikErrors<FormikValues>
12 |   touched?: FormikTouched<FormikValues>
13 | }
14 | 
15 | function ScenarioCardContainment({ errors, touched }: ScenarioCardContainmentProps) {
16 |   const { t } = useTranslation()
17 | 
18 |   return (
19 |     <CollapsibleCard
20 |       className="card-mitigation"
21 |       defaultCollapsed={false}
22 |       identifier="containmentScenario"
23 |       title={<h3 className="p-0 d-inline text-truncate">{t('Mitigation')}</h3>}
24 |       help={t(
25 |         'Reduction of transmission through mitigation measures over time. Add or remove interventions. The intervention efficacy is specified as a range of plausible multiplicative reductions of the base growth rate',
26 |       )}
27 |     >
28 |       <div className="w-auto">
29 |         <MitigationTable />
30 |       </div>
31 |     </CollapsibleCard>
32 |   )
33 | }
34 | 
35 | export { ScenarioCardContainment }
36 | 


--------------------------------------------------------------------------------
/src/i18n/detectLocale.ts:
--------------------------------------------------------------------------------
 1 | import { LocaleKey } from './i18n'
 2 | 
 3 | type NavigatorPlus = Navigator & { browserLanguage?: string; userLanguage?: string; systemLanguage?: string }
 4 | 
 5 | export interface DetectLanguageParams {
 6 |   defaultLanguage: LocaleKey
 7 |   availableLocales: LocaleKey[]
 8 |   shorten?: boolean
 9 | }
10 | 
11 | export function detectLocale({ defaultLanguage, availableLocales, shorten = true }: DetectLanguageParams): LocaleKey {
12 |   if (typeof navigator === 'undefined') {
13 |     return defaultLanguage
14 |   }
15 | 
16 |   const navigatorLocal = (navigator ?? window.navigator) as NavigatorPlus | undefined
17 | 
18 |   let language
19 |   if (navigatorLocal?.languages && navigatorLocal.languages.length > 0) {
20 |     language = navigatorLocal.language[0] ?? navigatorLocal.language
21 |   } else {
22 |     language =
23 |       navigatorLocal?.browserLanguage ??
24 |       navigatorLocal?.userLanguage ??
25 |       navigatorLocal?.systemLanguage ??
26 |       defaultLanguage
27 |   }
28 | 
29 |   if (!language) {
30 |     language = defaultLanguage
31 |   }
32 | 
33 |   if (shorten) {
34 |     language = language.slice(0, 2)
35 |   }
36 | 
37 |   if (availableLocales.includes(language as LocaleKey)) {
38 |     return language as LocaleKey
39 |   }
40 | 
41 |   return defaultLanguage
42 | }
43 | 


--------------------------------------------------------------------------------
/src/components/Form/FormRangeSpinBox.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import { Col, FormGroup, Row } from 'reactstrap'
 4 | 
 5 | import { getFormikErrors } from '../../helpers/getFormikErrors'
 6 | 
 7 | import type { FormSpinBoxProps } from './FormSpinBox'
 8 | 
 9 | import FormLabel from './FormLabel'
10 | import { RangeSpinBox } from './RangeSpinBox'
11 | 
12 | export function FormRangeSpinBox<T>({
13 |   identifier,
14 |   label,
15 |   help,
16 |   step,
17 |   min,
18 |   max,
19 |   pattern,
20 |   errors,
21 |   touched,
22 | }: FormSpinBoxProps<T>) {
23 |   const errorMessages = getFormikErrors({ identifier, errors, touched })
24 |   const hasError = errorMessages.length > 0
25 | 
26 |   return (
27 |     <FormGroup inline className="my-0">
28 |       <Row noGutters>
29 |         <Col xl={6}>
30 |           <FormLabel identifier={identifier} label={label} help={help} />
31 |         </Col>
32 |         <Col className="d-inline" xl={6}>
33 |           <RangeSpinBox identifier={identifier} step={step} min={min} max={max} pattern={pattern} hasError={hasError} />
34 | 
35 |           {errorMessages.map((message) => (
36 |             <div key={message} className="text-danger">
37 |               {message}
38 |             </div>
39 |           ))}
40 |         </Col>
41 |       </Row>
42 |     </FormGroup>
43 |   )
44 | }
45 | 


--------------------------------------------------------------------------------
/src/components/Main/Controls/PlotControls.tsx:
--------------------------------------------------------------------------------
 1 | import React from 'react'
 2 | 
 3 | import { useTranslation } from 'react-i18next'
 4 | 
 5 | import FormSwitch from '../../Form/FormSwitch'
 6 | 
 7 | export interface PlotControlsProps {
 8 |   isLogScale: boolean
 9 |   toggleLogScale(): void
10 |   shouldFormatNumbers: boolean
11 |   toggleFormatNumbers(): void
12 | }
13 | 
14 | function PlotControls({ isLogScale, toggleLogScale, shouldFormatNumbers, toggleFormatNumbers }: PlotControlsProps) {
15 |   const { t } = useTranslation()
16 | 
17 |   return (
18 |     <>
19 |       <div className="mr-4" data-testid="LogScaleSwitch">
20 |         <FormSwitch
21 |           identifier="logScale"
22 |           label={t('Log scale')}
23 |           help={t('Toggle between logarithmic and linear scale on vertical axis of the plot')}
24 |           checked={isLogScale}
25 |           onValueChanged={toggleLogScale}
26 |         />
27 |       </div>
28 |       <div data-testid="HumanizedValuesSwitch">
29 |         <FormSwitch
30 |           identifier="showHumanized"
31 |           label={t('Format numbers')}
32 |           help={t('Show numerical results in a human friendly format')}
33 |           checked={shouldFormatNumbers}
34 |           onValueChanged={toggleFormatNumbers}
35 |         />
36 |       </div>
37 |     </>
38 |   )
39 | }
40 | 
41 | export { PlotControls }
42 | 


--------------------------------------------------------------------------------
/stylelint.config.js:
--------------------------------------------------------------------------------
 1 | require('./config/dotenv')
 2 | 
 3 | module.exports = {
 4 |   defaultSeverity: 'warning',
 5 |   extends: [
 6 |     'stylelint-config-standard',
 7 |     'stylelint-config-css-modules',
 8 |     'stylelint-config-primer',
 9 | 
10 |     // stylelint-scss goes after everything else
11 |     'stylelint-config-recommended-scss',
12 | 
13 |     // prettier goes last
14 |     'stylelint-config-prettier',
15 |   ],
16 |   plugins: [
17 |     'stylelint-declaration-block-no-ignored-properties',
18 |     'stylelint-high-performance-animation',
19 |     'stylelint-no-indistinguishable-colors',
20 | 
21 |     // stylelint-scss goes after everything else
22 |     'stylelint-scss',
23 | 
24 |     // prettier goes last
25 |     'stylelint-prettier',
26 |   ],
27 |   rules: {
28 |     'plugin/declaration-block-no-ignored-properties': true,
29 |     'plugin/no-low-performance-animation-properties': true,
30 |     'plugin/no-unsupported-browser-features': null, // disable feature checks: we use postcss-preset-env and autoprefixer
31 |     'plugin/stylelint-no-indistinguishable-colors': true,
32 | 
33 |     'no-descending-specificity': [true, { ignore: ['selectors-within-list'] }],
34 |     'prettier/prettier': true,
35 |     'selector-max-compound-selectors': 4,
36 |     'selector-max-specificity': '0,5,1',
37 |     'selector-max-type': null,
38 |   },
39 | }
40 | 


--------------------------------------------------------------------------------
/data/parsers/okinawa.py:
--------------------------------------------------------------------------------
 1 | import sys
 2 | import requests
 3 | import csv
 4 | import io
 5 | from datetime import datetime
 6 | 
 7 | from .utils import store_data, stoi
 8 | 
 9 | # ------------------------------------------------------------------------
10 | # Globals
11 | 
12 | #URL  = "https://github.com/spigolotti/covid2019data_okinawa/okinawaCOVID19.csv"
13 | URL = "https://github.com/spigolotti/covid2019data_okinawa/blob/master/okinawaCOVID19.csv?raw=true"
14 | cols = ['time', 'cases', 'deaths', 'hospitalized', 'icu', 'recovered']
15 | 
16 | # ------------------------------------------------------------------------
17 | # Main point of entry
18 | 
19 | def parse():
20 |     r  = requests.get(URL)
21 |     if not r.ok:
22 |         print(f"Failed to fetch {URL}", file=sys.stderr)
23 |         exit(1)
24 |         r.close()
25 |     regions = {'JPN-Okinawa': []}   
26 |     fd  = io.StringIO(r.text)
27 |     rdr = csv.reader(fd)
28 |     hdr = next(rdr)
29 |     for row in rdr:
30 |         if len(row[0])==0:
31 |             continue
32 |         date_str=row[0]
33 |         num_cases = stoi(row[1])
34 |         num_deaths = stoi(row[2])
35 |         num_hosp = stoi(row[3])
36 |         num_recover = stoi(row[5])
37 |         regions["JPN-Okinawa"].append([date_str, num_cases, num_deaths, num_hosp, None, num_recover])
38 | 
39 |     store_data(regions, 'okinawa', cols)
40 | 


--------------------------------------------------------------------------------
/src/io/defaults/getAgeDistributionData.ts:
--------------------------------------------------------------------------------
 1 | import { AgeDistributionArray, AgeDistributionData, Convert } from '../../algorithms/types/Param.types'
 2 | import validateAgeDistributionArray, { errors } from '../../.generated/latest/validateAgeDistributionArray'
 3 | import ageDistributionRaw from '../../assets/data/ageDistribution.json'
 4 | 
 5 | function validate(): AgeDistributionData[] {
 6 |   const valid = validateAgeDistributionArray(ageDistributionRaw)
 7 |   if (!valid) {
 8 |     throw errors
 9 |   }
10 | 
11 |   return ((ageDistributionRaw as unknown) as AgeDistributionArray).all
12 | }
13 | 
14 | const ageDistributions = validate()
15 | export const ageDistributionNames = ageDistributions.map((cad) => cad.name)
16 | 
17 | export function getAgeDistributionData(name: string) {
18 |   const ageDistributionFound = ageDistributions.find((cad) => cad.name === name)
19 |   if (!ageDistributionFound) {
20 |     throw new Error(`Error: country age distribution "${name}" not found in JSON`)
21 |   }
22 | 
23 |   const ageDistribution = Convert.toAgeDistributionData(JSON.stringify(ageDistributionFound))
24 | 
25 |   ageDistribution.data.sort((a, b) => {
26 |     if (a.ageGroup > b.ageGroup) {
27 |       return +1
28 |     }
29 | 
30 |     if (a.ageGroup < b.ageGroup) {
31 |       return -1
32 |     }
33 | 
34 |     return 0
35 |   })
36 | 
37 |   return ageDistribution
38 | }
39 | 


--------------------------------------------------------------------------------