From b3d375f19e05a41dc91cb599582b6834e03109d3 Mon Sep 17 00:00:00 2001 From: Jonathan Clem Date: Mon, 4 May 2020 14:29:37 -0400 Subject: [PATCH] Initial commit --- .babelrc | 14 + .dockerignore | 2 + .env.build.example | 1 + .env.example | 14 + .gitattributes | 1 + .github/workflows/db-migrate.yml | 25 + .github/workflows/deploy.yml | 24 + .github/workflows/fetch-recorded-data.yml | 39 + .github/workflows/lint.yml | 23 + .github/workflows/test.yml | 23 + .github/workflows/validate-models.yml | 21 + .gitignore | 7 + .vscode/settings.json | 16 + CODE_OF_CONDUCT.md | 128 + CONTRIBUTING.md | 35 + Dockerfile | 8 + LICENSE | 21 + PROJECT-INTENT.md | 26 + README.md | 181 + SECURITY.md | 3 + components/AppFrame.tsx | 17 + components/Button.module.css | 16 + components/Button.tsx | 18 + components/CaseSummary.tsx | 95 + components/ChartWrapper.tsx | 236 + components/Disclaimer.tsx | 48 + components/IncompleteSimulation.tsx | 17 + components/LocalDate.tsx | 18 + components/LocalTime.tsx | 18 + components/ModelInfo.module.css | 50 + components/ModelInfo.tsx | 56 + components/ModelSelect.tsx | 27 + components/NavBar.module.css | 16 + components/NavBar.tsx | 29 + components/OutboundLink.tsx | 11 + components/OutcomeChart/Interventions.tsx | 267 + components/OutcomeChart/LegendSparkline.tsx | 138 + components/OutcomeChart/OutcomeChart.tsx | 721 + .../OutcomeChart/OutcomeChartActual.tsx | 47 + components/OutcomeChart/OutcomeChartFlag.tsx | 47 + components/OutcomeChart/OutcomeChartHover.tsx | 98 + .../OutcomeChartInterventions.tsx | 38 + .../OutcomeChart/OutcomeChartLegendBlock.tsx | 123 + components/OutcomeChart/OutcomeChartLine.tsx | 88 + components/OutcomeChart/OutcomeChartXAxis.tsx | 74 + components/OutcomeChart/OutcomeChartYAxis.tsx | 66 + components/OutcomeChart/SVGLinePattern.tsx | 38 + components/OutcomeChart/chartColors.ts | 11 + components/ResultTable.module.css | 31 + components/ResultTable.tsx | 32 + components/ResultTables.tsx | 91 + components/ResultViewSettings.tsx 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lib/github.ts | 92 + lib/handle-error.ts | 32 + lib/logging.ts | 55 + lib/models.ts | 54 + lib/mysql.ts | 70 + lib/new-simulation-state.ts | 405 + lib/redirect.ts | 18 + lib/regionEmoji.ts | 9 + lib/sentry.ts | 97 + lib/session.ts | 125 + lib/simulation-schema.ts | 105 + lib/simulation-types.ts | 69 + migrations/.gitkeep | 0 ...331170118-create-simulations-runs-table.js | 59 + .../20200331210801-create-locations-table.js | 53 + ...dd-github-user-login-to-simulation-runs.js | 59 + ...9-drop-location-id-from-simulation-runs.js | 59 + .../20200402165728-create-regions-table.js | 59 + ...d-iso-region-columns-to-simulation-runs.js | 59 + .../20200402172411-drop-locations-table.js | 59 + .../20200402181839-insert-default-region.js | 59 + ...-add-workflow-run-id-to-simulation-runs.js | 53 + ...github-user-id-index-to-simulation-runs.js | 53 + migrations/20200406180709-rename-uk-to-gb.js | 53 + .../20200406183238-create-authorized-users.js | 53 + .../20200406191215-insert-us-subregions.js | 53 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...add-model-runs-to-simulation-runs-down.sql | 21 + ...2-add-model-runs-to-simulation-runs-up.sql | 14 + ...456-add-admin-to-authorized-users-down.sql | 1 + ...74456-add-admin-to-authorized-users-up.sql | 1 + ...26-add-config-to-authorized-users-down.sql | 1 + ...1526-add-config-to-authorized-users-up.sql | 1 + ...3859-add-label-to-simulation-runs-down.sql | 1 + ...153859-add-label-to-simulation-runs-up.sql | 1 + ...51-create-intervention-data-table-down.sql | 1 + ...5151-create-intervention-data-table-up.sql | 17 + ...0430164001-add-new-europe-regions-down.sql | 42 + ...200430164001-add-new-europe-regions-up.sql | 41 + models.yml | 55 + next-env.d.ts | 2 + next.config.js | 80 + now.json | 38 + now.prod.json | 38 + package-lock.json | 16768 ++++++++++++++++ package.json | 177 + pages/_app.tsx | 101 + pages/_document.tsx | 19 + pages/about.module.css | 30 + pages/about.tsx | 98 + pages/api/callback.ts | 69 + pages/api/login.ts | 24 + pages/api/logout.ts | 15 + pages/api/simulations/[id]/case-summary.ts | 106 + pages/api/simulations/[id]/download.ts | 68 + pages/api/simulations/[id]/index.ts | 59 + pages/api/simulations/index.ts | 137 + pages/api/types/async-next-api-handler.ts | 5 + pages/api/user/accept-disclaimer.ts | 17 + pages/api/util/blob-storage.ts | 41 + pages/api/util/dispatch.ts | 57 + pages/api/util/require-session.ts | 16 + pages/index.module.css | 17 + pages/index.tsx | 20 + pages/logout.tsx | 11 + pages/meta/_boom.tsx | 100 + pages/simulations/[id].tsx | 322 + pages/simulations/index.module.css | 9 + pages/simulations/index.tsx | 62 + pages/simulations/new.module.css | 77 + pages/simulations/new.tsx | 43 + pages/simulations/simulation.module.css | 65 + pages/unauthorized.tsx | 14 + postcss.config.js | 16 + public/images/google.png | Bin 0 -> 1236 bytes script/authorize-local-user | 14 + script/db-console | 5 + script/db-create | 5 + script/db-migrate | 5 + script/fetch-recorded-data | 282 + script/server | 5 + script/setup | 95 + script/staging-alias | 5 + svg/Check.svg | 3 + svg/Chevron.svg | 3 + svg/CircleCheck.svg | 3 + svg/Clock.svg | 4 + svg/Code.svg | 3 + svg/Cross.svg | 3 + svg/Descartes.svg | 8 + svg/Dot.svg | 1 + svg/Download.svg | 3 + svg/Failure.svg | 4 + svg/Fork.svg | 3 + svg/GitHub.svg | 3 + svg/Info.svg | 3 + svg/Link.svg | 3 + svg/Plus.svg | 4 + svg/Pushpin.svg | 7 + svg/Share.svg | 3 + svg/SocialDistancingGraphic.svg | 17 + svg/StatusSpinner.svg | 4 + svg/Success.svg | 3 + svg/Trash.svg | 3 + svg/Unacast.svg | 22 + svg/Warn.svg | 3 + svg/Zip.svg | 3 + tailwind.config.js | 102 + test/dateFunctions.test.ts | 73 + test/new-simulation-state.test.ts | 337 + test/tsconfig.json | 5 + tsconfig.json | 20 + types/case-data.ts | 12 + types/hospital-data.ts | 12 + types/index.d.ts | 1 + types/model-runner.ts | 149 + types/regions.d.ts | 41 + 257 files changed, 46187 insertions(+) create mode 100644 .babelrc create mode 100644 .dockerignore create mode 100644 .env.build.example create mode 100644 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create mode 100644 svg/CircleCheck.svg create mode 100644 svg/Clock.svg create mode 100644 svg/Code.svg create mode 100644 svg/Cross.svg create mode 100644 svg/Descartes.svg create mode 100644 svg/Dot.svg create mode 100644 svg/Download.svg create mode 100644 svg/Failure.svg create mode 100644 svg/Fork.svg create mode 100644 svg/GitHub.svg create mode 100644 svg/Info.svg create mode 100644 svg/Link.svg create mode 100644 svg/Plus.svg create mode 100644 svg/Pushpin.svg create mode 100644 svg/Share.svg create mode 100644 svg/SocialDistancingGraphic.svg create mode 100644 svg/StatusSpinner.svg create mode 100644 svg/Success.svg create mode 100644 svg/Trash.svg create mode 100644 svg/Unacast.svg create mode 100644 svg/Warn.svg create mode 100644 svg/Zip.svg create mode 100644 tailwind.config.js create mode 100644 test/dateFunctions.test.ts create mode 100644 test/new-simulation-state.test.ts create mode 100644 test/tsconfig.json create mode 100644 tsconfig.json create mode 100644 types/case-data.ts create mode 100644 types/hospital-data.ts create mode 100644 types/index.d.ts create mode 100644 types/model-runner.ts create mode 100644 types/regions.d.ts diff --git a/.babelrc b/.babelrc new file mode 100644 index 0000000..0cae859 --- /dev/null +++ b/.babelrc @@ -0,0 +1,14 @@ +{ + "presets": [ + [ + "next/babel", + { + "preset-env": {}, + "transform-runtime": {}, + "styled-jsx": {}, + "class-properties": {} + } + ] + ], + "plugins": ["inline-react-svg"] +} diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..55890fe --- /dev/null +++ b/.dockerignore @@ -0,0 +1,2 @@ +/.next/ +/node_modules/ diff --git a/.env.build.example b/.env.build.example new file mode 100644 index 0000000..691928d --- /dev/null +++ b/.env.build.example @@ -0,0 +1 @@ +GITHUB_CLIENT_ID=$LOCALHOST_GITHUB_CLIENT_ID diff --git a/.env.example b/.env.example new file mode 100644 index 0000000..9aabd19 --- /dev/null +++ b/.env.example @@ -0,0 +1,14 @@ +GITHUB_CLIENT_ID=$LOCALHOST_GITHUB_CLIENT_ID +GITHUB_CLIENT_SECRET=$LOCALHOST_GITHUB_CLIENT_SECRET +GITHUB_API_TOKEN=$GITHUB_PERSONAL_ACCESS_TOKEN_WITH_REPO_SCOPE +RUNNER_SHARED_SECRET=runner-shared-secret +RUNNER_CALLBACK_URL=$RUNNER_CALLBACK_PROXY_URL +CONTROL_REPO_NWO=covid-modeling/prod-covid19-control-plane +CONTROL_REPO_EVENT_TYPE=test-run-simulation +BLOB_STORAGE_ACCOUNT=$BLOB_STORAGE_ACCOUNT +BLOB_STORAGE_KEY=$BLOB_STORAGE_KEY +# Arbitrary session secret generated via `openssl rand -hex 32` +OAUTH_SECRET=9984beb4f8c53cea0dd4bb8c59c747f49bb5622d16dac8040228d2b0669c0385 +# Arbitrary session secret generated via `openssl rand -hex 32` +SESSION_SECRET=4afd67b10fadfa8d4216425343120541c5c65f23b1d188230bf32a97d1a54e15 +LOCAL_MODE=true diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..b4e0121 --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +migrations/*.js linguist-generated=true diff --git a/.github/workflows/db-migrate.yml b/.github/workflows/db-migrate.yml new file mode 100644 index 0000000..f587de2 --- /dev/null +++ b/.github/workflows/db-migrate.yml @@ -0,0 +1,25 @@ +on: + repository_dispatch: + types: db-migrate + +jobs: + deploy: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - run: | + echo "Client Payload:" + echo '${{toJson(github.event.client_payload)}}' + - run: | + docker-compose -f docker-compose.yml -f docker-compose.db.yml run \ + -e DB_USERNAME="${{secrets.DB_USERNAME}}" \ + -e DB_PASSWORD="${{secrets.DB_PASSWORD}}" \ + -e DB_HOST="${{secrets.DB_HOST}}" \ + -e DB_DATABASE="${{secrets.DB_DATABASE}}" \ + -e DB_USERNAME_STAGING="${{secrets.DB_USERNAME_STAGING}}" \ + -e DB_PASSWORD_STAGING="${{secrets.DB_PASSWORD_STAGING}}" \ + -e DB_HOST_STAGING="${{secrets.DB_HOST_STAGING}}" \ + -e DB_DATABASE_STAGING="${{secrets.DB_DATABASE_STAGING}}" \ + db-migrate ${{github.event.client_payload.direction}} \ + --env ${{github.event.client_payload.env}} \ + --count ${{github.event.client_payload.count}} diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml new file mode 100644 index 0000000..fdebbe4 --- /dev/null +++ b/.github/workflows/deploy.yml @@ -0,0 +1,24 @@ +on: + repository_dispatch: + types: deploy + +jobs: + deploy: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - uses: actions/cache@v1 + with: + path: ~/.npm + key: ${{runner.os}}-deploy-${{hashFiles('**/package-lock.json')}} + - run: npm ci + - run: | + mkdir .now + echo '{"projectId":"${{secrets.ZEIT_PROJECT_ID}}","orgId":"${{secrets.ZEIT_ORG_ID}}"}' > .now/project.json + - run: npx now --token ${{secrets.ZEIT_TOKEN}} -b GITHUB_SHA=${{github.sha}} --prod -A now.prod.json + - run: | + npx sentry-cli \ + --auth-token "${{secrets.SENTRY_AUTH_TOKEN}}" \ + releases --org github-disease-modelling \ + deploys "${{github.sha}}" \ + new -e production diff --git a/.github/workflows/fetch-recorded-data.yml b/.github/workflows/fetch-recorded-data.yml new file mode 100644 index 0000000..32ee208 --- /dev/null +++ b/.github/workflows/fetch-recorded-data.yml @@ -0,0 +1,39 @@ +on: + schedule: + # covidtracking.com updates at 4pm, we run at 5pm for some wiggle room. + - cron: '0 21 * * *' + repository_dispatch: + types: fetch-recorded-data + +jobs: + fetch-recorded-data: + name: Fetch recorded case and intervention data + runs-on: ubuntu-latest + env: + NODE_ENV: production + steps: + - uses: actions/checkout@v2 + - uses: actions/cache@v1 + with: + path: ~/.npm + key: ${{runner.os}}-deploy-${{hashFiles('**/package-lock.json')}} + - uses: actions/setup-node@v1 + with: + node-version: 13.x + - run: npm ci + - run: | + echo "Updating recorded data in staging database..." + script/fetch-recorded-data + env: + DB_USERNAME: ${{ secrets.DB_USERNAME_STAGING }} + DB_PASSWORD: ${{ secrets.DB_PASSWORD_STAGING }} + DB_HOST: ${{ secrets.DB_HOST_STAGING }} + DB_DATABASE: ${{ secrets.DB_DATABASE_STAGING }} + - run: | + echo "Updating recorded data in production database..." + script/fetch-recorded-data + env: + DB_USERNAME: ${{ secrets.DB_USERNAME }} + DB_PASSWORD: ${{ secrets.DB_PASSWORD }} + DB_HOST: ${{ secrets.DB_HOST }} + DB_DATABASE: ${{ secrets.DB_DATABASE }} diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml new file mode 100644 index 0000000..1ec6941 --- /dev/null +++ b/.github/workflows/lint.yml @@ -0,0 +1,23 @@ +name: Lint + +on: + pull_request: + branches: master + +jobs: + lint: + name: Run lint + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - uses: actions/cache@v1 + with: + path: ~/.npm + key: ${{runner.os}}-deploy-${{hashFiles('**/package-lock.json')}} + - uses: actions/setup-node@v1 + with: + node-version: 13.x + - run: npm ci + - run: npx tsc --noEmit + - run: git fetch --no-tags --prune --depth=1 origin +refs/heads/master + - run: npx eslint $(git diff-index --name-only --diff-filter=AM origin/master -- "*.js" "*.jsx" "*.ts" "*.tsx") diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..461f244 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,23 @@ +name: Test + +on: + pull_request: + branches: master + +jobs: + lint: + name: Run Tests + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - uses: actions/cache@v1 + with: + path: ~/.npm + key: ${{runner.os}}-deploy-${{hashFiles('**/package-lock.json')}} + - uses: actions/setup-node@v1 + with: + node-version: 13.x + - run: npm ci + - run: npx tsc --noEmit + - run: git fetch --no-tags --prune --depth=1 origin +refs/heads/master + - run: npm test diff --git a/.github/workflows/validate-models.yml b/.github/workflows/validate-models.yml new file mode 100644 index 0000000..d09e348 --- /dev/null +++ b/.github/workflows/validate-models.yml @@ -0,0 +1,21 @@ +name: Validate Models + +on: + push: {branches: master} + pull_request: {branches: master} + +jobs: + validate_models: + name: Validate Models + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - uses: actions/cache@v1 + with: + path: ~/.npm + key: ${{runner.os}}-deploy-${{hashFiles('**/package-lock.json')}} + - run: npm ci + - run: | + npx ts-json-schema-generator -p lib/models.ts -t ModelMap -o schema.json + npx js-yaml models.yml > models.json + npx ajv validate -s schema.json -d models.json diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..4fd2347 --- /dev/null +++ b/.gitignore @@ -0,0 +1,7 @@ +/.next/ +/node_modules/ +!/.vscode/ +.now +.env +.env.build +now.local.json diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..f9fa2f9 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,16 @@ +{ + "editor.codeActionsOnSave": { + "source.organizeImports": true + }, + "editor.formatOnSave": true, + "files.exclude": { + "**/.next": true + }, + "search.exclude": { + "**/.next": true + }, + "files.watcherExclude": {}, + "prettier.semi": false, + "prettier.singleQuote": true, + "prettier.bracketSpacing": false +} diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..bb64741 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,128 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, religion, or sexual identity +and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +- Demonstrating empathy and kindness toward other people +- Being respectful of differing opinions, viewpoints, and experiences +- Giving and gracefully accepting constructive feedback +- Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +- Focusing on what is best not just for us as individuals, but for the + overall community + +Examples of unacceptable behavior include: + +- The use of sexualized language or imagery, and sexual attention or + advances of any kind +- Trolling, insulting or derogatory comments, and personal or political attacks +- Public or private harassment +- Publishing others' private information, such as a physical or email + address, without their explicit permission +- Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +opensource@github.com. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series +of actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or +permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within +the community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.0, available at +[https://www.contributor-covenant.org/version/2/0/code_of_conduct.html]. + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see the FAQ at +[https://www.contributor-covenant.org/faq]. Translations are available at +[https://www.contributor-covenant.org/translations]. diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..330daa2 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,35 @@ +## Contributing + +[fork]: https://github.com/covid-modeling/web/fork +[pr]: https://github.com/covid-modeling/web/compare +[style]: https://github.com/google/gts +[code-of-conduct]: CODE_OF_CONDUCT.md + +Hi there! We're thrilled that you'd like to contribute to this project. Your help is essential for keeping it great. + +Contributions to this project are [released](https://help.github.com/articles/github-terms-of-service/#6-contributions-under-repository-license) to the public under the [MIT license](LICENSE). + +Please note that this project is released with a [Contributor Code of Conduct][code-of-conduct]. By participating in this project you agree to abide by its terms. + +## Submitting a pull request + +0. [Fork][fork] and clone the repository +1. Configure and install the dependencies. +2. Make sure the tests pass on your machine. +3. Create a new branch: `git checkout -b my-branch-name` +4. Make your change, add tests, and make sure the tests still pass +5. Push to your fork and [submit a pull request][pr] +6. Pat your self on the back and wait for your pull request to be reviewed and merged. + +Here are a few things you can do that will increase the likelihood of your pull request being accepted: + +- Follow the [style guide][style]. +- Write tests. +- Keep your change as focused as possible. If there are multiple changes you would like to make that are not dependent upon each other, consider submitting them as separate pull requests. +- Write a [good commit message](http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html). + +## Resources + +- [How to Contribute to Open Source](https://opensource.guide/how-to-contribute/) +- [Using Pull Requests](https://help.github.com/articles/about-pull-requests/) +- [GitHub Help](https://help.github.com) diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..98384f6 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,8 @@ +FROM node:13-alpine + +WORKDIR /app +COPY script script +COPY package*.json ./ +RUN npm ci + +CMD ["npm", "run", "dev"] diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..5b2d1ff --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2020 GitHub + +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the "Software"), to deal in +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies +of the Software, and to permit persons to whom the Software is furnished to do +so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/PROJECT-INTENT.md b/PROJECT-INTENT.md new file mode 100644 index 0000000..53d0c98 --- /dev/null +++ b/PROJECT-INTENT.md @@ -0,0 +1,26 @@ +# Covid modeling UI + +## What +The Covid modeling UI is a tool for policy makers to experiment with mitigation strategies, running each strategy through several models and comparing the projections. The mitigation strategies specify what policies are in force at any given time, and the models project the likely number of deaths, infections, hospitalisations and ICU use. + +## Why? +By examining the projections of multiple models, policy makers can gain an understanding of the level of uncertainty and divergence of expert opinion. In cases where models disagree, this can provide the basis for informed discussion between policy makers and epidemiologists on the deeper reasons for such discrepancies. + +## Who +The UI was originally designed in a collaboration between potential users, modeling experts, a team of engineers at GitHub, and the AI+Cloud strategy team at Microsoft. + +## Goals +The code is made available here to enable modelers to extend the breadth and depth of the information provided to policy makers, in particular by adding: +- models, to give the broadest coverage of epidemiological expertise, +- intervention types, such as various testing strategies and contact tracing, +- data sources for displaying “ground truth” alongside future projections, such as past intervention policies and mobility data, +- geographies not currently supported by the models that have already been integrated, +- ways to compare models, for example through new visualisations or by scoring their fit to the ground truth. + +We welcome contributions in all five of these areas. See [CONTRIBUTING.md](CONTRIBUTING.md). + +Currently the service running the simulations has restricted access because some of the simulations are compute-intensive to run. We are however firm believers in the need to share the data, and we’d therefore welcome contributions to make pre-computed projections for common scenarios visible to the general public. + + +## Non-goals +Of course there are other potential applications of this code, such as a more sophisticated UI for experts to experiment with all the advanced parameters of a particular model. We’d be glad to see those applications in forks of this repository. diff --git a/README.md b/README.md new file mode 100644 index 0000000..007f7e5 --- /dev/null +++ b/README.md @@ -0,0 +1,181 @@ +# GitHub COVID Modelling Web UI [![.github/workflows/deploy.yml](https://github.com/covid-modeling/web/workflows/.github/workflows/deploy.yml/badge.svg?branch=master)](https://github.com/covid-modeling/web/actions?query=branch%3Amaster) + +This is a [Next.js][nextjs] application that serves the GitHub +COVID modelling web interface. It is hosted on [Vercel][vercel]. + +The needs of the unified modelling project are changing rapidly, and so we do +not have a set-in-stone development roadmap. This application is built with +the goal of it hopefully being not too difficult to alter or even rewrite +parts of it as requirements change. + +To learn more about this project's goals, please see [PROJECT-INTENT.md](PROJECT-INTENT.md) + +## Local Development + +This app has two development modes: "local" and "advanced" mode. The "local" +mode is a much easier development setup, but does not actually queue +simulation runs with the development control plane. Instead, it uses a +stubbed result. The "advanced" mode is for maintainers only—it requires +access to some shared credentials and accounts. + +### Shared Setup (for both local and advanced modes) + +1. Install and start [Docker][docker]. +1. Get the [GitHub OAuth development app][oauth] client ID and secret. You'll be prompted for them shortly. +1. Clone this repository: + + ```shell + > git clone https://github.com/covid-modeling/web + > cd web + ``` + +1. Install dependencies: + + ```shell + > npm install + ``` + +### Local Mode Setup + +1. Run the environment setup script: + + ```shell + > script/setup + ``` + + This script will ask you a series of questions—you'll want to answer that + yes, you do want to run in local mode. + +1. Start the server: + + ```shell + > script/server + ``` + +1. Fetch case data: + + This script requires some environment variables (see + `script/fetch-recorded-data --help`), but if you've already got your .env + set up, you can run the script with [foreman][foreman] to avoid manually + setting them: + + ```shell + > npx foreman run script/fetch-recorded-data + ``` + +1. Authorize your local user to log in: + + ```shell + > script/authorize-local-user $my_github_username + ``` + +### Advanced Mode Setup (Maintainers Only) + +Advanced mode requires a number of secrets documented in [env.yml](env.yml), +whose development values can be accessed by following instructions in the +private [maintainers-only documentation][maintainer-docs]. + +1. Start an HTTP [ngrok proxy][ngrok] pointing to port 3000 and + note its URL (such as "https://e028f3f1.ngrok.io"): + + ```shell + > ngrok http 3000 + ``` + +1. Run the environment setup script: + + ```shell + > script/setup + ``` + + This script will ask you a series of questions—you'll want to answer that + no, you don't want to run in local mode. + + This script will now ask for a number of environment variables, each of + which can be accessed by following instructions in the [maintainer + docs][maintainer-docs]. + + It'll also ask you for a `RUNNER_CALLBACK_URL`, which should be the value of + your ngrok proxy. + +1. Start the server: + + ```shell + > script/server + ``` + +1. Fetch case data: + + This script requires some environment variables (see + `script/fetch-recorded-data --help`), but if you've already got your .env + set up, you can run the script with [foreman][foreman] to avoid manually + setting them: + + ```shell + > npx foreman run script/fetch-recorded-data + ``` + +1. Authorize your local user to log in: + + ```shell + > script/authorize-local-user $my_github_username + ``` + +### Database & Migrations + +In development, database migrations are run automatically when the web +container starts. + +To create a database migration: + +```shell +# Create a migration +> script/db-migrate create name-of-migration --sql-file +``` + +We pass the `--sql-file` here because we write migrations in plain SQL in +this project. + +### Environment Variables + +Environment variables are documented in [env.yml](env.yml). + +## Architecture + +- Pages are in `pages/{route}.tsx`. +- Components are in `components/{Component}.tsx`. +- API functions are in `pages/api/{route}.tsx`. + +### Useful Documentation + +- [Next.js pages](https://nextjs.org/docs/basic-features/pages) +- [Next.js API routes](https://nextjs.org/docs/api-routes/introduction) +- [Vercel serverless functions](https://zeit.co/docs/v2/serverless-functions/introduction) +- [Vercel environment variables and secrets](https://zeit.co/docs/v2/serverless-functions/env-and-secrets) +- [React documentation](https://reactjs.org/docs/getting-started.html) + +## Updating Case Data and Intervention Data + +The `case_data` and `intervention_data` tables are populated by the `fetch-recorded-data` script. +This is run nightly on staging and production. + +## Contributing + +We welcome contributions to this project from the community. See +[CONTRIBUTING.md](CONTRIBUTING.md). + +## License + +This project is licensed under the MIT license. See [LICENSE](LICENSE). + +[docker]: https://app.datadoghq.com/logs?saved_view=86476 +[dpx]: https://npm.im/dpx +[foreman]: https://npm.im/foreman +[maintainer-docs]: https://github.com/covid-modeling/project-docs-internal/blob/master/docs/web-operations.md +[nextjs]: https://nextjs.org +[ngrok]: https://ngrok.com/ +[oauth]: https://github.com/organizations/covid-modeling/settings/applications/1253529 +[prod]: https://covid-modeling.org +[staging]: https://staging.covid-modeling.org +[vercel]: https://vercel.com +[vercel-org]: https://zeit.co/covid-modeling diff --git a/SECURITY.md b/SECURITY.md new file mode 100644 index 0000000..2218838 --- /dev/null +++ b/SECURITY.md @@ -0,0 +1,3 @@ +If you discover a security issue in this repo, please submit it through the [GitHub Security Bug Bounty](https://hackerone.com/github) + +Thanks for helping make Covid Modeling safe for everyone. diff --git a/components/AppFrame.tsx b/components/AppFrame.tsx new file mode 100644 index 0000000..6b9e30b --- /dev/null +++ b/components/AppFrame.tsx @@ -0,0 +1,17 @@ +import {PropsWithChildren} from 'react' +import NavBar from './NavBar' + +type Props = { + loggedIn: boolean +} + +export default function AppFrame(props: PropsWithChildren) { + return ( +
+
+ +
+
{props.children}
+
+ ) +} diff --git a/components/Button.module.css b/components/Button.module.css new file mode 100644 index 0000000..d4c516c --- /dev/null +++ b/components/Button.module.css @@ -0,0 +1,16 @@ +.Button { + @apply inline-block; +} + +.ButtonContent { + @apply flex items-center justify-center; + @apply bg-black; + @apply rounded; + @apply text-sm text-white; + + padding: 0.9rem 1rem; +} + +.Button svg { + @apply mr-4; +} diff --git a/components/Button.tsx b/components/Button.tsx new file mode 100644 index 0000000..0212e9e --- /dev/null +++ b/components/Button.tsx @@ -0,0 +1,18 @@ +import styles from './Button.module.css' + +type Props = { + icon?: JSX.Element + text: string + className?: string +} + +export default function Button(props: Props) { + return ( + + + {props.icon} + {props.text} + + + ) +} diff --git a/components/CaseSummary.tsx b/components/CaseSummary.tsx new file mode 100644 index 0000000..8bd2311 --- /dev/null +++ b/components/CaseSummary.tsx @@ -0,0 +1,95 @@ +import {AxiosError} from 'axios' +import useSWR from 'swr' +import models from '../lib/models' +import {CaseSummary as CaseSummaryType} from '../pages/api/simulations/[id]/case-summary' +import LocalDate from './LocalDate' +import StatusBlock from './StatusBlock' +import Table from './Table' + +type Props = { + simulationID: number +} + +export default function CaseSummary(props: Props) { + const {data, error} = useSWR, AxiosError>( + `/api/simulations/${props.simulationID}/case-summary`, + { + revalidateOnFocus: false, + revalidateOnReconnect: false + } + ) + + if (error) { + return ( +
+ +

+ Error loading simulation case summary. +

+ +
+ ) + } + + if (!data) { + return ( +
+ +

Loading simulation case summary...

+ +
+ ) + } + + return ( + + + + + {Object.keys(data).map(modelSlug => ( + + ))} + + + + + + + {Object.entries(data).map(([slug, summary]) => ( + + ))} + + + + + {Object.entries(data).map(([slug, summary]) => ( + + ))} + + + + + {Object.entries(data).map(([slug, summary]) => ( + + ))} + + + + + {Object.entries(data).map(([slug, summary]) => ( + + ))} + + + + + {Object.entries(data).map(([slug, summary]) => ( + + ))} + + +
Summary{models[modelSlug].name}
Cumulative confirmed cases{summary.cConf.toLocaleString()}
Cumulative hospitalizations{summary.cHosp.toLocaleString()}
Cumulative deaths{summary.cDeaths.toLocaleString()}
Peak deaths date + +
Peak daily deaths{summary.peakDailyDeath.toLocaleString()}
+ ) +} diff --git a/components/ChartWrapper.tsx b/components/ChartWrapper.tsx new file mode 100644 index 0000000..25891e1 --- /dev/null +++ b/components/ChartWrapper.tsx @@ -0,0 +1,236 @@ +import {DateTime} from 'luxon' +import {useMemo, useState} from 'react' +import {animated, useSpring} from 'react-spring' +import USCapacityData from '../data/hospitals/us.json' +import {cumsum, elementSum} from '../lib/arrayMath' +import {ModelRun, Simulation} from '../lib/db' +import {CaseData} from '../types/case-data' +import {ModelOutput, RunStatus, SeverityMetrics} from '../types/model-runner' +import ModelSelect from './ModelSelect' +import OutcomeChart, { + OutcomeChartConfiguration, + ScaleXDomainMonths, + ScaleYType +} from './OutcomeChart/OutcomeChart' +import ResultViewSettings from './ResultViewSettings' + +const AnimatedOutcomeChart = animated(OutcomeChart) + +export type ToggleGroupOption = { + label: string + value: number | string | null + disabled?: boolean +} + +interface Props { + regionID: string + regionName: string + subregionID: string | undefined + subregionName: string | undefined + simulation: Simulation + modelRun: ModelRun + result: ModelOutput + caseData: CaseData + onChangeModel: (slug: string) => void +} + +export default function ChartWrapper(props: Props) { + const {result} = props + + // figure out what timerange options to offer + const t0 = DateTime.fromISO(result.time.t0, {zone: 'utc'}) + const extentEnd = result.time.extent[1] + + // Figure out which time toggle options to offer + // and which to choose by default + const [timeToggleOptions, defaultTimeToggleValue]: [ + ToggleGroupOption[], + number | null + ] = useMemo(() => { + const tMaxEverything = t0.plus({days: extentEnd}) + const tMaxDiff = tMaxEverything.diff(t0, 'months') + const timeToggleOptions = [ + { + label: '6 Months', + value: 6, + disabled: tMaxDiff.months < 6 + }, + { + label: '12 Months', + value: 12, + disabled: tMaxDiff.months < 12 + }, + { + label: 'Full Range', + value: null, + disabled: false + } + ] + let defaultTimeToggleValue: number | null = null + // default to the first not-disabled one + for (const o of timeToggleOptions) { + if (!o.disabled) { + defaultTimeToggleValue = o.value as number | null + break + } + } + return [timeToggleOptions, defaultTimeToggleValue] + }, [t0, extentEnd]) + + const config: OutcomeChartConfiguration[][] = useMemo(() => { + let normalBedsCapacity, icuBedsCapacity + if (result.metadata.region === 'US' && result.metadata.subregion) { + const stateAbbr = result.metadata.subregion.slice(-2) + const state = USCapacityData.find(s => s.abbr === stateAbbr) + if (state) { + normalBedsCapacity = Math.floor( + (state.total_beds - state.icu_beds) * (1 - state.utilization) + ) + icuBedsCapacity = Math.floor(state.icu_beds * (1 - state.utilization)) + } + } + return [ + [ + { + title: 'Deaths', + color: 'black', + projected: { + values: 'incDeath', + cumulative: (metrics: SeverityMetrics) => cumsum(metrics.incDeath) + }, + actual: { + values: 'deaths', + cumulative: 'cumulativeDeaths' + } + } + ], + [ + { + title: 'Infections', + color: 'blue', + projected: { + values: (metrics: SeverityMetrics) => + elementSum([ + metrics.Mild, + metrics.ILI, + metrics.SARI, + metrics.Critical + ]), + cumulative: (metrics: SeverityMetrics) => + elementSum([ + metrics.cumMild, + metrics.cumILI, + metrics.cumSARI, + metrics.cumCritical + ]) + }, + actual: { + values: 'confirmed', + cumulative: 'cumulativeConfirmed', + name: 'Confirmed' + } + } + ], + [ + { + title: 'Normal Hospital Beds', + color: 'purple', + projected: { + values: (metrics: SeverityMetrics) => + elementSum([metrics.SARI, metrics.CritRecov]), + cumulative: (metrics: SeverityMetrics) => + elementSum([metrics.cumSARI, metrics.cumCritRecov]) + }, + capacity: normalBedsCapacity + }, + { + title: 'Intensive Care Beds', + color: 'orange', + projected: { + values: 'Critical', + cumulative: 'cumCritical' + }, + capacity: icuBedsCapacity + }, + { + title: 'Ventilators Required', + color: 'pink', + projected: { + values: (metrics: SeverityMetrics) => + metrics.Critical.map(m => m / 2), + cumulative: (metrics: SeverityMetrics) => + metrics.cumCritical.map(m => m / 2) + } + } + ] + ] + }, [result]) + + // Shared chart state + const [hoverX, setHoverX] = useState(null) + const [hoverInterventionIdx, setHoverIntervention] = useState( + null + ) + const [pinnedInterventionIdx, setPinnedIntervention] = useState< + number | null + >(null) + const [scaleYType, setScaleYType] = useState('linear') + const [cumulative, setCumulative] = useState(false) + const [scaleXDomainMonths, setScaleXDomainMonths] = useState< + ScaleXDomainMonths + >(defaultTimeToggleValue) + + const tMax = t0 + .plus( + scaleXDomainMonths + ? {months: scaleXDomainMonths} + : {days: result.time.extent[1]} + ) + .toMillis() + const {tMaxMillis} = useSpring({ + tMaxMillis: tMax + }) + + const sharedHandlerState = { + hoverX, + onHoverX: setHoverX, + hoverInterventionIdx, + onHoverIntervention: setHoverIntervention, + pinnedInterventionIdx, + onPinIntervention: setPinnedIntervention, + scaleYType, + cumulative, + scaleXDomainMonths + } + + return ( +
+
+ r.model_slug)} + onChange={props.onChangeModel} + /> + + +
+ + +
+ ) +} diff --git a/components/Disclaimer.tsx b/components/Disclaimer.tsx new file mode 100644 index 0000000..e0f2944 --- /dev/null +++ b/components/Disclaimer.tsx @@ -0,0 +1,48 @@ +import Axios from 'axios' +import {useRouter} from 'next/router' +import {useContext, useState} from 'react' +import {SentryContext} from '../pages/_app' +import CircleCheck from '../svg/CircleCheck.svg' +import btnStyles from './styles/button.module.css' + +export default function Disclaimer() { + const router = useRouter() + const {captureException} = useContext(SentryContext) + const [error, setError] = useState(null) + + // TODO: Currently this is only a UI block—the API will still return results. + const acceptDisclaimer = async () => { + try { + setError(null) + await Axios.post('/api/user/accept-disclaimer') + router.reload() + } catch (err) { + captureException(err) + setError('An unexpected error occurred.') + } + } + + return ( +
+ {error ?

{error}

: null} +

+ These results are based on simulations from different modeling groups. + Results are subject to change as real world situations change over time and more data is available. + These results are not medical predictors and are provided as-is. + The models themselves, their underlying assumptions, and their weaknesses + should be reviewed carefully before making any decisions. +

+ + +
+ ) +} diff --git a/components/IncompleteSimulation.tsx b/components/IncompleteSimulation.tsx new file mode 100644 index 0000000..83a5aab --- /dev/null +++ b/components/IncompleteSimulation.tsx @@ -0,0 +1,17 @@ +import {RunStatus} from '../types/model-runner' +import StatusBlock from './StatusBlock' + +interface Props { + status: RunStatus.Pending | RunStatus.InProgress | RunStatus.Failed + title: string + message: string +} + +export default function IncompleteSimulation(props: Props) { + return ( + +

{props.title}

+

{props.message}

+ + ) +} diff --git a/components/LocalDate.tsx b/components/LocalDate.tsx new file mode 100644 index 0000000..062f6ad --- /dev/null +++ b/components/LocalDate.tsx @@ -0,0 +1,18 @@ +import {DateTime} from 'luxon' +import {ISODate} from '../types/model-runner' + +type Props = { + isoDate: ISODate +} + +export default function LocalDate(props: Props) { + return ( + + ) +} diff --git a/components/LocalTime.tsx b/components/LocalTime.tsx new file mode 100644 index 0000000..e608af0 --- /dev/null +++ b/components/LocalTime.tsx @@ -0,0 +1,18 @@ +type Props = { + time: Date + options?: Intl.DateTimeFormatOptions +} + +export default function LocalTime(props: Props) { + return ( + + ) +} diff --git a/components/ModelInfo.module.css b/components/ModelInfo.module.css new file mode 100644 index 0000000..0e90c7e --- /dev/null +++ b/components/ModelInfo.module.css @@ -0,0 +1,50 @@ +.largecontainer { + @apply flex flex-col; + @apply mr-6; + @apply p-4; + @apply w-full; + @apply rounded; + @apply border; + @apply shadow-sm; + min-height: 310px; + background-image: linear-gradient(180deg, #ffffff 0%, #fbfbfc 100%); +} + +.minimalcontainer { + @apply flex; + @apply mr-6; + @apply w-full; +} + +.container:nth-child(2) { + @apply mr-0; +} + +.container h1, +.container h2 { + @apply leading-relaxed; +} + +.container p { + @apply flex-1; + @apply mt-4; + @apply text-sm; + color: #2f3037; +} + +.largecontainer .links { + @apply mt-12; +} + +.container .links a { + @apply mr-4; + @apply inline-block; +} +.container .links a svg { + @apply mr-3; + @apply inline; + @apply relative; + @apply align-middle; + bottom: 1px; + color: #9194a1; +} diff --git a/components/ModelInfo.tsx b/components/ModelInfo.tsx new file mode 100644 index 0000000..b39b1a0 --- /dev/null +++ b/components/ModelInfo.tsx @@ -0,0 +1,56 @@ +import {MinimalModelSpec, ModelSpec} from '../lib/models' +import Code from '../svg/Code.svg' +import Link from '../svg/Link.svg' +import styles from './ModelInfo.module.css' +import OutboundLink from './OutboundLink' +import btnStyles from './styles/button.module.css' + +type Props = { + modelSpec: ModelSpec | MinimalModelSpec + minimal?: boolean +} + +export default function ModelInfo(props: Props) { + const spec = props.modelSpec + const fullSpec = spec as ModelSpec + const links = spec.metaURLs + + return ( +
+ {!props.minimal && ( + <> +

{fullSpec.name}

+

{fullSpec.origin}

+

{fullSpec.description}

+ + )} + +
+ {links?.paper ? ( + + + Read the paper + + ) : null} + + {links?.website ? ( + + + Website + + ) : null} + + {links?.code ? ( + + + Code + + ) : null} +
+
+ ) +} diff --git a/components/ModelSelect.tsx b/components/ModelSelect.tsx new file mode 100644 index 0000000..594ccbb --- /dev/null +++ b/components/ModelSelect.tsx @@ -0,0 +1,27 @@ +import models from '../lib/models' +import selectStyle from './styles/select.module.css' + +type Props = { + modelSlug: keyof typeof models + modelOpts: (keyof typeof models)[] + onChange: (modelSlug: string) => void +} + +export default function ModelSelect(props: Props) { + return ( + + ) +} diff --git a/components/NavBar.module.css b/components/NavBar.module.css new file mode 100644 index 0000000..21b8735 --- /dev/null +++ b/components/NavBar.module.css @@ -0,0 +1,16 @@ +.NavBar { + @apply flex items-center; + @apply h-14 w-full; + @apply px-8; + @apply bg-black; + @apply text-sm text-white; +} + +.NavBar h1 { + @apply uppercase; + @apply mr-5; +} + +.NavBarContent { + @apply flex-1; +} diff --git a/components/NavBar.tsx b/components/NavBar.tsx new file mode 100644 index 0000000..c2479b3 --- /dev/null +++ b/components/NavBar.tsx @@ -0,0 +1,29 @@ +import Link from 'next/link' +import {PropsWithChildren} from 'react' +import styles from './NavBar.module.css' + +type Props = { + loggedIn: boolean +} + +export default function NavBar(props: PropsWithChildren) { + return ( +
+

+ + Covid Simulator + +

+ +
{props.children}
+ +

+ + About + +

+ + {props.loggedIn && Log out} +
+ ) +} diff --git a/components/OutboundLink.tsx b/components/OutboundLink.tsx new file mode 100644 index 0000000..fb74254 --- /dev/null +++ b/components/OutboundLink.tsx @@ -0,0 +1,11 @@ +import {PropsWithChildren} from 'react' + +type Props = Omit + +const OutboundLink = (props: PropsWithChildren) => ( + + {props.children} + +) + +export default OutboundLink diff --git a/components/OutcomeChart/Interventions.tsx b/components/OutcomeChart/Interventions.tsx new file mode 100644 index 0000000..78970a8 --- /dev/null +++ b/components/OutcomeChart/Interventions.tsx @@ -0,0 +1,267 @@ +import {DateTime} from 'luxon' +import React, {FunctionComponent, useMemo} from 'react' +import {Intervention} from './OutcomeChart' + +type InterventionsProps = { + interventions: Intervention[] + trackHeight: number + scaleX: d3.ScaleTime + hoverDate: DateTime + pinnedInterventionIdx: number | null + hoverInterventionIdx: number | null + height: number + width: number + chartsHeight: number +} + +const Interventions: FunctionComponent = ({ + interventions, + trackHeight, + scaleX, + hoverDate, + pinnedInterventionIdx, + hoverInterventionIdx, + height, + width, + chartsHeight +}) => { + const separators = useMemo( + () => ( + + {interventions.map((i, idx) => { + const y = chartsHeight + idx * trackHeight + return ( + + ) + })} + + ), + [interventions, width, chartsHeight, trackHeight] + ) + + const hoverLine = useMemo(() => { + const hoverDateX = scaleX(hoverDate) + return ( + + ) + }, [scaleX, hoverDate, chartsHeight, height]) + + const [hoverSpans, hoverSpines] = useMemo(() => { + let spans: JSX.Element[] = [] + let spines: JSX.Element[] = [] + for (let iIdx = 0; iIdx < interventions.length; iIdx++) { + const intervention = interventions[iIdx] + const hovering = iIdx === hoverInterventionIdx + const pinned = iIdx === pinnedInterventionIdx + const display = pinned || (hovering && pinnedInterventionIdx === null) + const y = chartsHeight + iIdx * trackHeight + + spans = spans.concat( + intervention.ranges.map((r, rIdx) => { + const startX = scaleX(r.start.toMillis()) + const endX = scaleX(r.end.toMillis()) + return ( + + ) + }) + ) + spines = spines.concat( + intervention.ranges.map((r, rIdx) => { + const startX = scaleX(r.start.toMillis()) + return ( + + ) + }) + ) + } + return [spans, spines] + }, [ + chartsHeight, + height, + hoverInterventionIdx, + interventions, + pinnedInterventionIdx, + scaleX, + trackHeight + ]) + + const [interventionSpans, interventionSpines] = useMemo(() => { + let spans: JSX.Element[] = [] + let spines: JSX.Element[] = [] + for (let iIdx = 0; iIdx < interventions.length; iIdx++) { + const intervention = interventions[iIdx] + const y = chartsHeight + iIdx * trackHeight + const deemphasized = + (hoverInterventionIdx ?? pinnedInterventionIdx) !== null && + iIdx !== hoverInterventionIdx && + iIdx !== pinnedInterventionIdx + spans = spans.concat( + intervention.ranges.map((r, rIdx) => { + const startX = scaleX(r.start.toMillis()) + const endX = scaleX(r.end.toMillis()) + return ( + + ) + }) + ) + spines = spines.concat( + intervention.ranges.map((r, rIdx) => { + const startX = scaleX(r.start.toMillis()) + return ( + + ) + }) + ) + } + return [spans, spines] + }, [ + chartsHeight, + hoverInterventionIdx, + interventions, + pinnedInterventionIdx, + scaleX, + trackHeight + ]) + + const label = useMemo(() => { + const idx = pinnedInterventionIdx ?? hoverInterventionIdx + if (idx === null) { + return + } + const intervention = interventions[idx] + const y = chartsHeight + idx * trackHeight + return intervention.ranges.map((range, i) => { + const startX = scaleX(range.start.toMillis()) + if (hoverDate >= range.start && hoverDate < range.end) + return ( + + {range.start.toFormat('d LLL')} + + ) + }) + }, [ + chartsHeight, + hoverDate, + hoverInterventionIdx, + interventions, + pinnedInterventionIdx, + scaleX, + trackHeight + ]) + + return ( + + {/* render separators between tracks */} + {separators} + + {/* render bg hover spans */} + {hoverSpans} + + {/* render intervention spans */} + {interventionSpans} + + {/* render spines and hover spines */} + {interventionSpines} + {hoverSpines} + + {/* render label */} + {label} + + {/* render hover line */} + {hoverLine} + + ) +} + +export default React.memo(Interventions) diff --git a/components/OutcomeChart/LegendSparkline.tsx b/components/OutcomeChart/LegendSparkline.tsx new file mode 100644 index 0000000..bcfb7f8 --- /dev/null +++ b/components/OutcomeChart/LegendSparkline.tsx @@ -0,0 +1,138 @@ +import * as d3 from 'd3' +import {curveMonotoneX, ScaleLinear, ScaleLogarithmic, ScaleTime} from 'd3' +import React, {FunctionComponent, useMemo} from 'react' +import useSafeDimensions from '../../hooks/use-safe-dimensions' +import {ChartColors, ChartColorsType} from './chartColors' +import {Datum} from './OutcomeChart' + +type LegendSparklineProps = { + data: Datum[] + scaleX: ScaleTime + scaleY: + | ScaleLinear + | ScaleLogarithmic + tMax: number + color: ChartColorsType + hoverIdx: number +} + +const LegendSparkline: FunctionComponent = props => { + const {ref, dimensions} = useSafeDimensions() + + const [scaleX, tMaxX] = useMemo(() => { + // get a copy of the scale but set the range (pixels) + // for this component's dimensions + const sx = props.scaleX.copy().range([0, dimensions.width]) + // We want to grab a copy of the domain + // This sparkline will always display the full range of data + // but right now the domain max is affected by the time selector. + // The domain max is also animated over time when changing. + // We can cache the value of it here. + const visibleDomain = sx.domain() + // Set the domain to include the entirety of the data + sx.domain([visibleDomain[0], props.tMax]) + // return the scale with the new domain and the x coord of the + // max visible timestamp from the full chart + return [sx, sx(visibleDomain[1])] + }, [props.scaleX, props.tMax, dimensions]) + + const scaleY = useMemo( + () => props.scaleY.copy().rangeRound([dimensions.height - 3, 1.5]), + [props.scaleY, dimensions] + ) + + const line = useMemo( + () => + d3 + .line() + .curve(curveMonotoneX) + // Typescript seems to think that Number.isFinite(null) is wrong + // But actually Typescript is wrong and should feel wrong. + .defined(d => Number.isFinite(d.y as number)) + .x(d => scaleX(d.x)) + // Well, the type definitions for line.y are simply wrong + // D3 has a built-in notion of undefined handling, see .defined + // but .y()'s typedef signature expects an fn that returns a number + .y(d => scaleY(d.y as number)), + [scaleX, scaleY] + ) + + const hover = useMemo(() => { + const hoverY = props.data[props.hoverIdx].y + if (hoverY !== null) { + return ( + + ) + } + }, [scaleX, scaleY, props.data, props.color, props.hoverIdx]) + + const bg = useMemo( + () => ( + + ), + [dimensions] + ) + + const visibleIndicator = useMemo( + () => ( + + ), + [tMaxX, dimensions] + ) + + const path = useMemo( + () => ( + + ), + [line, props.data, props.color] + ) + + return ( +
+ + {bg} + {visibleIndicator} + {path} + {hover} + +
+ ) +} + +export default React.memo(LegendSparkline) diff --git a/components/OutcomeChart/OutcomeChart.tsx b/components/OutcomeChart/OutcomeChart.tsx new file mode 100644 index 0000000..461dec7 --- /dev/null +++ b/components/OutcomeChart/OutcomeChart.tsx @@ -0,0 +1,721 @@ +import classNames from 'classnames' +import * as d3 from 'd3' +import {ScaleLinear, ScaleLogarithmic, ScaleTime} from 'd3' +import {DateTime} from 'luxon' +import {FunctionComponent, useMemo} from 'react' +import useSafeDimensions from '../../hooks/use-safe-dimensions' +import {maxIndex} from '../../lib/arrayMath' +import {StrategyDescriptions, StrategyKey} from '../../lib/new-simulation-state' +import Pushpin from '../../svg/Pushpin.svg' +import {CaseData} from '../../types/case-data' +import {Intensity, ModelOutput, SeverityMetrics} from '../../types/model-runner' +import {ChartColors, ChartColorsType} from './chartColors' +import Interventions from './Interventions' +import OutcomeChartActual from './OutcomeChartActual' +import OutcomeChartFlag from './OutcomeChartFlag' +import OutcomeChartHover from './OutcomeChartHover' +import OutcomeChartLegendBlock from './OutcomeChartLegendBlock' +import OutcomeChartLine from './OutcomeChartLine' +import OutcomeChartXAxis from './OutcomeChartXAxis' +import OutcomeChartYAxis from './OutcomeChartYAxis' +import SVGLinePattern from './SVGLinePattern' + +type KeyOrMetricsAccessor = string | ((m: SeverityMetrics) => number[]) +type KeyOrCaseDataAccessor = string | ((m: CaseData) => number[]) +export type ScaleYType = 'linear' | 'logarithmic' +export type ScaleXDomainMonths = number | null + +export type OutcomeChartConfiguration = { + title: string + color: ChartColorsType + projected: { + values: KeyOrMetricsAccessor + cumulative: KeyOrMetricsAccessor + variance?: KeyOrMetricsAccessor + incidence?: KeyOrMetricsAccessor + } + actual?: { + values: KeyOrCaseDataAccessor + cumulative: KeyOrCaseDataAccessor + name?: string + } + capacity?: number +} + +export type PreparedMetricsSeries = { + title: string + color: ChartColorsType + projectedPeak: DateTime + projected: { + values: Datum[] + cumulative: Datum[] + variance?: Datum[] + incidence?: Datum[] + } + actual?: { + values: Datum[] + cumulative: Datum[] + name?: string + } + capacity?: number + y: number +} + +type OutcomeChartProps = { + result: ModelOutput + caseData?: CaseData + title?: string + config: OutcomeChartConfiguration[][] + hoverX: number | null + hoverInterventionIdx: number | null + pinnedInterventionIdx: number | null + scaleYType: ScaleYType + cumulative: boolean + scaleXDomainMonths: ScaleXDomainMonths + scaleXAnimatedMax: number + onHoverX: (x: number | null) => void + onHoverIntervention: (idx: number | null) => void + onPinIntervention: (idx: number | null) => void +} + +export type Intervention = { + title: string + ranges: { + start: DateTime + end: DateTime + degree: Intensity + }[] +} + +export type Datum = { + x: number + y: number | null +} + +const interventionTrackHeight = 25 +const seriesHeight = 128 + +const OutcomeChart: FunctionComponent = ({ + result, + config, + hoverX, + hoverInterventionIdx, + pinnedInterventionIdx, + scaleYType, + cumulative, + scaleXAnimatedMax, + onHoverX, + onHoverIntervention, + onPinIntervention, + caseData +}) => { + const {ref, dimensions} = useSafeDimensions() + + // We want to use naïve dates everywhere + // So actually using UTC dates + // "Today" is whatever today's date is for the user + // But we need the same 'wall calendar' date in UTC + // so convert to string and reparse :facepalm: + const today = DateTime.fromISO( + DateTime.local() + .startOf('day') + .toISODate(), + {zone: 'utc'} + ) + + const t0 = useMemo(() => DateTime.fromISO(result.time.t0, {zone: 'utc'}), [ + result.time.t0 + ]) + + const tEnd = useMemo(() => t0.plus({days: result.time.extent[1]}), [ + t0, + result.time.extent + ]) + + // Prepare interventions + const interventions: Intervention[] = useMemo(() => { + const interventionPeriods = result.metadata.parameters.interventionPeriods + const interventions: Record = { + schoolClosure: {title: 'School Closures', ranges: []}, + socialDistancing: {title: 'Social Distancing', ranges: []}, + caseIsolation: {title: 'Case Isolation', ranges: []}, + voluntaryHomeQuarantine: { + title: 'Voluntary Home Quarantine', + ranges: [] + } + } + for (let i = 0; i < interventionPeriods.length; i++) { + const period = interventionPeriods[i] + const end = + i + 1 === interventionPeriods.length + ? tEnd + : DateTime.fromISO(interventionPeriods[i + 1].startDate, { + zone: 'utc' + }) + const start = DateTime.fromISO(period.startDate, { + zone: 'utc' + }) + + Object.keys(StrategyDescriptions).forEach(k => { + const degree = period[k as StrategyKey] + if (degree) { + interventions[k as StrategyKey].ranges.push({ + start, + end, + degree + }) + } + }) + } + return Object.values(interventions) + }, [result, tEnd]) + + // intervention rows are each interventionTrackHeight pixels tall + const chartsHeight = + dimensions.height === 0 + ? 0 + : dimensions.height - interventions.length * interventionTrackHeight + + // converts a numeric array into date/value tuples + // Configs are an array of groups. Each group will render a chart. + // Each group can contain one or more series. Each series will render a line. + const prepared: PreparedMetricsSeries[][] = useMemo(() => { + // Map()able fn to convert a number[] into datum[] + const datumize = (d: number | null, i: number) => ({ + x: t0.plus({days: result.time.timestamps[i]}).toMillis(), + // guard against negative numbers here + // They sometimes happen in fatality data from JHU + y: typeof d === 'number' ? (!(d < 0) ? d : 0) : d + }) + + // Locate the peak date for a given series + const peakDate = (arr: (number | null)[]) => + t0.plus({ + days: result.time.timestamps[maxIndex(arr)] + }) + + const prepareProjected = (k: KeyOrMetricsAccessor): Datum[] => { + // if it's a key name, pluck that metric and datumize + // if we were handed an accessor, use that to fetch the series to datumize + switch (typeof k) { + case 'string': + return result.aggregate.metrics[k as keyof SeverityMetrics].map( + datumize + ) + + case 'function': + return k(result.aggregate.metrics).map(datumize) + } + } + + const prepareActual = (k: KeyOrCaseDataAccessor): Datum[] => { + if (!caseData) + throw 'Tried to prepare actual casedata but it was not available.' + switch (typeof k) { + case 'string': + return caseData[k as keyof CaseData].map(datumize) + case 'function': + return k(caseData).map(datumize) + } + } + + // a memo for the y offset of each series + // because there are G groups each containing S series + // calculating the top offset of each series requires doing + // seriesHeight * total number of previous series in previous groups + // this is super side-effect-y but practical ¯\_(ツ)_/¯ + let y = 0 + return config.map(group => + group.map(series => { + const projected = { + values: prepareProjected(series.projected.values), + cumulative: prepareProjected(series.projected.cumulative), + variance: series.projected.variance + ? prepareProjected(series.projected.variance) + : undefined, + incidence: series.projected.incidence + ? prepareProjected(series.projected.incidence) + : undefined + } + let actual + if (series.actual) { + actual = { + values: prepareActual(series.actual.values), + cumulative: prepareActual(series.actual.cumulative), + name: series.actual.name + } + } + + const preparedSeries: PreparedMetricsSeries = { + title: series.title, + color: series.color, + capacity: series.capacity, + projectedPeak: peakDate(projected.values.map(d => d.y)), + projected, + actual, + y + } + y += seriesHeight + return preparedSeries + }) + ) + }, [config, caseData, result.aggregate.metrics, result.time.timestamps, t0]) + + // compute the extent of the values across all series in a group + // assumes that there's some data + const extents = useMemo( + () => + prepared.map(group => + d3.extent( + group + .map(series => + cumulative + ? [series.projected.cumulative, series?.actual?.cumulative] + : [series.projected.values, series?.actual?.values] + ) + .flat(2) + .filter(d => d !== undefined), + d => d.y + ) + ), + [prepared, cumulative] + ) as [[number, number]] + + // prepare scales + // X is shared across everything + const scaleX: ScaleTime = useMemo( + () => + d3 + .scaleUtc() + .domain([ + t0.plus({days: result.time.extent[0]}).toMillis(), + scaleXAnimatedMax + ]) + .range([0, dimensions.width]), + [t0, result, dimensions, scaleXAnimatedMax] + ) + + // Y is shared within a group + const scalesY: + | ScaleLinear[] + | ScaleLogarithmic[] = useMemo( + () => + extents.map(e => { + switch (scaleYType) { + case 'linear': + return d3 + .scaleLinear() + .domain(e) + .range([seriesHeight, 0]) + .nice() + case 'logarithmic': + return ( + d3 + .scaleLog() + // log10(0) = -infinity + // that sucks from a rendering perspective + // and our lower extent is almost always 0 + // so force it to be 1, and clamp all input values + // e.g. force scaleY(v) to be scaleY(1) for v < 1 + .domain([e[0] === 0 ? 1 : e[0], e[1]]) + .range([seriesHeight, 0]) + .clamp(true) + .nice() + ) + } + }), + [extents, scaleYType] + ) + + // compute X hover index and date + // hoverIdx is the index into the array of metrics + // hoverDate is the date computed using the index and the array of + // timestamp offsets + const [hoverIdx, hoverDate] = useMemo(() => { + // We are using "UTC Dates" as a kind of zoneless date everywhere + // lalala I can't see no timezones can't hear you + // d3 scaleTime.invert returns a JS Date, which we don't want + // but the millis since epoch is correct since that's UTC + // use them to index into our array of timestamps + // and then use that index to generate the appropriate UTC Date + const hoverDate = hoverX ? +scaleX.invert(hoverX) : today.toMillis() + const i = d3.bisectLeft( + prepared[0][0].projected.values.map(d => d.x), + hoverDate + ) + // we deal in round dates + // coerce hoverdates to the start of the relevant day + return [i, t0.plus({days: result.time.timestamps[i]}).startOf('day')] + }, [hoverX, scaleX, prepared, today, result.time.timestamps, t0]) + + const todayX = useMemo(() => scaleX(today.toMillis()), [today, scaleX]) + + const whichIntervention = ( + e: React.MouseEvent + ) => { + const rect = e.currentTarget.getBoundingClientRect() + const localY = e.clientY - rect.y + return localY > chartsHeight + ? Math.floor((localY - chartsHeight) / interventionTrackHeight) + : null + } + + const handleMouseX = (e: React.MouseEvent) => { + switch (e.type) { + case 'mouseleave': + onHoverX(null) + break + + default: + onHoverX(e.clientX - e.currentTarget.getBoundingClientRect().x) + break + } + } + + const handleMouseXY = (e: React.MouseEvent) => { + switch (e.type) { + case 'mouseleave': + onHoverX(null) + onHoverIntervention(null) + break + + default: + const rect = e.currentTarget.getBoundingClientRect() + onHoverX(e.clientX - rect.x) + onHoverIntervention(whichIntervention(e)) + break + } + } + + const handleMouseClick = ( + e: React.MouseEvent + ) => { + const intervention = whichIntervention(e) + if (intervention !== null) { + // unpin if clicked, otherwise pin the one that's clicked. + onPinIntervention( + intervention === pinnedInterventionIdx ? null : intervention + ) + } + } + + return ( +
+
+
+
+ {!hoverX && ( +
+ Today + {hoverDate.toFormat('LLL d, yyyy')} +
+ )} +   +
+ {prepared.map((group, i) => + group.map(series => ( +
+ +
+ )) + )} + +
+ {interventions.map((i, idx) => { + const hovering = idx === hoverInterventionIdx + const pinned = idx == pinnedInterventionIdx + return ( +
onHoverIntervention(idx)} + onMouseLeave={() => onHoverIntervention(null)} + onClick={() => onPinIntervention(pinned ? null : idx)} + > +
{i.title}
+
+ +
+
+ ) + })} +
+
+
+ + +
+ + + + + + + {/* + Draw interventions part of the chart + They're at the bottom (Y) of the chart, + but we want them to render behind everything else + So we're rendering them earlier in the SVG. + */} + + + {/* Render the today line and line shading of the past */} + + + + {/* + Draw each chart group + For ease of math, draw in a that is translated to the right y coord + so each chart can pretend it is drawing from 0,0 + + But actually... + Do this three times so we draw all the different layers + SVG doesn't respect z-index, only drawn order (later = above) + + So, draw: + - All the separator lines & Y axes + - All the data lines + - All the hovers + */} + + {/* Separator lines & Y axes */} + {prepared.map((group, groupIdx) => + group.map(series => { + const capacityY = + !cumulative && series.capacity + ? scalesY[groupIdx](series.capacity) + : undefined + return ( + + + + {!!capacityY && + capacityY > 0 && + capacityY < seriesHeight && ( + + + + Capacity + + + )} + + ) + }) + )} + + {/* Draw series projected + actuals data */} + {prepared.map((group, groupIdx) => + group.map(series => ( + + return ( + + {series.actual && ( + + )} + + + ) + + )) + )} + + {/* Draw hovers */} + {prepared + .map((group, groupIdx) => + group + .map((series, seriesIdx) => ( + + + + )) + .reverse() + ) + .reverse()} + +
+
+ +
+
+
+
+ ) +} + +export default OutcomeChart diff --git a/components/OutcomeChart/OutcomeChartActual.tsx b/components/OutcomeChart/OutcomeChartActual.tsx new file mode 100644 index 0000000..1686ce9 --- /dev/null +++ b/components/OutcomeChart/OutcomeChartActual.tsx @@ -0,0 +1,47 @@ +import * as d3 from 'd3' +import {curveMonotoneX, ScaleLinear, ScaleLogarithmic, ScaleTime} from 'd3' +import React, {FunctionComponent} from 'react' +import {ChartColorsType} from './chartColors' +import {Datum} from './OutcomeChart' + +type OutcomeChartActualProps = { + data: Datum[] + scaleX: ScaleTime + scaleY: + | ScaleLinear + | ScaleLogarithmic + height: number + color?: ChartColorsType +} + +const OutcomeChartActual: FunctionComponent = ({ + data, + scaleX, + scaleY, + height, + color = 'purple' +}) => { + const area = d3 + .area() + .curve(curveMonotoneX) + // Typescript seems to think that Number.isFinite(null) is wrong + // But actually Typescript is wrong and should feel wrong. + .defined(d => Number.isFinite(d.y as number)) + .x(d => scaleX(d.x)) + .y0(height) + // Well, the type definitions for line.y are simply wrong + // D3 has a built-in notion of undefined handling, see .defined + // but .y()'s typedef signature expects an fn that returns a number + .y1(d => scaleY(d.y as number)) + return ( + + + + ) +} + +export default React.memo(OutcomeChartActual) diff --git a/components/OutcomeChart/OutcomeChartFlag.tsx b/components/OutcomeChart/OutcomeChartFlag.tsx new file mode 100644 index 0000000..d0b95ee --- /dev/null +++ b/components/OutcomeChart/OutcomeChartFlag.tsx @@ -0,0 +1,47 @@ +import {DateTime} from 'luxon' +import React, {FunctionComponent} from 'react' +import useSafeDimensions from '../../hooks/use-safe-dimensions' + +type OutcomeChartFlagProps = { + scaleX: d3.ScaleTime + width: number + hoverDate: DateTime + today: DateTime +} + +const OutcomeChartFlag: FunctionComponent = ({ + scaleX, + width, + hoverDate, + today +}) => { + const {ref, dimensions} = useSafeDimensions() + const text = hoverDate.hasSame(today, 'day') + ? 'Today' + : hoverDate.toFormat('LLL d, yyyy') + const x = scaleX(hoverDate.toMillis()) + const left = x >= width - dimensions.width - 10 + return ( +
+
+ Today +
+
+ {text} +
+
+ ) +} + +export default React.memo(OutcomeChartFlag) diff --git a/components/OutcomeChart/OutcomeChartHover.tsx b/components/OutcomeChart/OutcomeChartHover.tsx new file mode 100644 index 0000000..1f045a1 --- /dev/null +++ b/components/OutcomeChart/OutcomeChartHover.tsx @@ -0,0 +1,98 @@ +import {ScaleLinear, ScaleLogarithmic, ScaleTime} from 'd3' +import React, {FunctionComponent} from 'react' +import {ChartColors} from './chartColors' +import {PreparedMetricsSeries} from './OutcomeChart' + +type OutcomeChartHoverProps = { + hoverIdx: number + scaleX: ScaleTime + scaleY: + | ScaleLinear + | ScaleLogarithmic + height: number + selector: 'cumulative' | 'values' + metrics: PreparedMetricsSeries +} + +const OutcomeChartHover: FunctionComponent = ({ + hoverIdx, + scaleX, + scaleY, + height, + metrics, + selector +}) => { + const hoverX = scaleX(metrics.projected[selector][hoverIdx].x) + + const yProjected = metrics.projected[selector][hoverIdx].y + const projectedMark = + yProjected === null ? ( + undefined + ) : ( + + + + + ) + + const yActual = metrics.actual?.[selector][hoverIdx].y + const actualMark = + typeof yActual === 'number' ? ( + + + + + ) : ( + undefined + ) + + return ( + + + {actualMark} + {projectedMark} + + ) +} + +export default React.memo(OutcomeChartHover) diff --git a/components/OutcomeChart/OutcomeChartInterventions.tsx b/components/OutcomeChart/OutcomeChartInterventions.tsx new file mode 100644 index 0000000..bc58363 --- /dev/null +++ b/components/OutcomeChart/OutcomeChartInterventions.tsx @@ -0,0 +1,38 @@ +import {ScaleTime} from 'd3' +import React, {FunctionComponent} from 'react' + +type OutcomeChartInterventionProps = { + dates: {start: Date; end: Date}[] + scaleX: ScaleTime + height: number +} + +const OutcomeChartIntervention: FunctionComponent = ({ + dates, + scaleX, + height +}) => { + return ( + + {dates.map(d => { + const x0 = scaleX(+d.start) + const x1 = scaleX(+d.end) + return ( + + ) + })} + + ) +} + +export default React.memo(OutcomeChartIntervention) diff --git a/components/OutcomeChart/OutcomeChartLegendBlock.tsx b/components/OutcomeChart/OutcomeChartLegendBlock.tsx new file mode 100644 index 0000000..0687406 --- /dev/null +++ b/components/OutcomeChart/OutcomeChartLegendBlock.tsx @@ -0,0 +1,123 @@ +import classNames from 'classnames' +import {ScaleLinear, ScaleLogarithmic, ScaleTime} from 'd3' +import numbro from 'numbro' +import React, {FunctionComponent, useMemo} from 'react' +import LegendSparkline from './LegendSparkline' +import {PreparedMetricsSeries} from './OutcomeChart' + +type OutcomeChartLegendBlockProps = { + series: PreparedMetricsSeries + selector: 'cumulative' | 'values' + hoverIdx: number + scaleX: ScaleTime + scaleY: + | ScaleLinear + | ScaleLogarithmic + tMax: number +} + +const OutcomeChartLegendBlock: FunctionComponent = ({ + series, + selector, + hoverIdx, + scaleX, + scaleY, + tMax +}) => { + const cumulative = selector === 'cumulative' + const [projectionExcess, projectedText] = useMemo(() => { + const projection = series.projected[selector][hoverIdx].y + let projectionExcess + if ( + !!projection && + !!series.capacity && + !cumulative && + projection > series.capacity + ) { + projectionExcess = numbro(projection - series.capacity).format({ + average: true, + totalLength: 3 + }) + } + const projectedText = + projection !== null + ? numbro(projection).format({ + thousandSeparated: true, + trimMantissa: true, + mantissa: 0 + }) + : 'No Data' + return [projectionExcess, projectedText] + }, [series, hoverIdx, cumulative, selector]) + + const [actualValueText, actualExcess] = useMemo(() => { + let actualValueText, actualExcess + if (series.actual) { + const actual = series.actual[selector][hoverIdx].y + if (actual !== undefined && actual !== null) { + actualValueText = numbro(actual).format({ + thousandSeparated: true, + trimMantissa: true, + mantissa: 0 + }) + if (!!series.capacity && !cumulative && actual > series.capacity) + actualExcess = numbro(actual - series.capacity).format({ + average: true, + totalLength: 3 + }) + } + } + return [actualValueText, actualExcess] + }, [series, hoverIdx, cumulative, selector]) + + return ( +
+
{'\u00A0'}
+
+
{series.title}
+
+ +
+
+
+ Projected +
+
{projectedText}
+ {projectionExcess && ( +
+ {projectionExcess} over +
+ )} +
+ {series.actual && ( +
+
+ {series.actual.name || 'Actual'} +
+
+ {actualValueText || 'No Data'} +
+ {actualExcess && ( +
+ {actualExcess} over +
+ )} +
+ )} +
+
+ ) +} + +export default React.memo(OutcomeChartLegendBlock) diff --git a/components/OutcomeChart/OutcomeChartLine.tsx b/components/OutcomeChart/OutcomeChartLine.tsx new file mode 100644 index 0000000..6f14776 --- /dev/null +++ b/components/OutcomeChart/OutcomeChartLine.tsx @@ -0,0 +1,88 @@ +import * as d3 from 'd3' +import {curveMonotoneX, ScaleLinear, ScaleLogarithmic, ScaleTime} from 'd3' +import React, {FunctionComponent, useMemo} from 'react' +import {ChartColors, ChartColorsType} from './chartColors' +import {Datum} from './OutcomeChart' + +type OutcomeChartLineProps = { + data: Datum[] + scaleX: ScaleTime + scaleY: + | ScaleLinear + | ScaleLogarithmic + color?: ChartColorsType + capacity?: number + cumulative: boolean +} + +const OutcomeChartLine: FunctionComponent = ({ + data, + scaleX, + scaleY, + color = 'purple', + capacity, + cumulative +}) => { + const line = useMemo(() => { + return ( + d3 + .line() + .curve(curveMonotoneX) + // Typescript seems to think that Number.isFinite(null) is wrong + // But actually Typescript is wrong and should feel wrong. + .defined(d => Number.isFinite(d.y as number)) + .x(d => scaleX(d.x)) + // Well, the type definitions for line.y are simply wrong + // D3 has a built-in notion of undefined handling, see .defined + // but .y()'s typedef signature expects an fn that returns a number + .y(d => scaleY(d.y as number)) + ) + }, [scaleX, scaleY]) + + const excess = useMemo(() => { + if (capacity && !cumulative) { + return d3 + .area() + .curve(curveMonotoneX) + .defined( + d => Number.isFinite(d.y as number) && (d.y as number) >= capacity + ) + .x(d => scaleX(d.x)) + .y1(d => scaleY(d.y as number)) + .y0(scaleY(capacity)) + } + }, [scaleX, scaleY, capacity, cumulative]) + + return ( + + {excess && ( + + + + + )} + + + ) +} + +export default React.memo(OutcomeChartLine) diff --git a/components/OutcomeChart/OutcomeChartXAxis.tsx b/components/OutcomeChart/OutcomeChartXAxis.tsx new file mode 100644 index 0000000..439ff80 --- /dev/null +++ b/components/OutcomeChart/OutcomeChartXAxis.tsx @@ -0,0 +1,74 @@ +import {ScaleTime, TimeInterval, timeMonth} from 'd3' +import {DateTime} from 'luxon' +import React, {FunctionComponent} from 'react' + +type OutcomeChartXAxisProps = { + scaleX: ScaleTime +} + +const OutcomeChartXAxis: FunctionComponent = ({ + scaleX +}) => { + const xTicksRaw = scaleX.ticks(timeMonth.every(1) as TimeInterval) + const xTicks = xTicksRaw.map((t, i) => { + const x = scaleX(t) + const dt = DateTime.fromJSDate(t) + let year + if (i === 0 || dt.year !== DateTime.fromJSDate(xTicksRaw[i - 1]).year) { + // if it's the first tick + // or the previous tick is from another year + // display the year on this tick + year = ( + + {dt.year} + + ) + } + return ( + + + + {DateTime.fromJSDate(t).toFormat('LLL')} + + {year} + + ) + }) + const height = 40 + return ( +
+ + {xTicks} + +
+ ) +} + +export default React.memo(OutcomeChartXAxis) diff --git a/components/OutcomeChart/OutcomeChartYAxis.tsx b/components/OutcomeChart/OutcomeChartYAxis.tsx new file mode 100644 index 0000000..4344e23 --- /dev/null +++ b/components/OutcomeChart/OutcomeChartYAxis.tsx @@ -0,0 +1,66 @@ +import {ScaleLinear, ScaleLogarithmic} from 'd3' +import numbro from 'numbro' +import React, {FunctionComponent} from 'react' +import {ScaleYType} from './OutcomeChart' + +type OutcomeChartYAxisProps = { + width: number + scaleY: + | ScaleLinear + | ScaleLogarithmic + type: ScaleYType +} + +const OutcomeChartYAxis: FunctionComponent = ({ + width, + scaleY, + type +}) => { + const yTicks = scaleY.ticks(5).map(t => { + const y = scaleY(t) + // for log scales, "round" ticks mean order-of-magnitude values + // e.g. 10, 100, 1000 + // log10(t) % 1 will be zero for these + // linear scale ticks will always be treated as "round" and rendered + // log scale ticks get special treatment only if round + const isRound = type === 'linear' ? true : !(Math.log10(t) % 1) + // if y is 0, we're drawing a tick above the top of the chart + // for 2nd chart groups and on, that bleeds into the chart above + // don't do that + if (y === 0) return + return ( + + + {isRound && ( + + {numbro(t).format({thousandSeparated: true})} + + )} + + ) + }) + + return {yTicks} +} + +export default React.memo(OutcomeChartYAxis) diff --git a/components/OutcomeChart/SVGLinePattern.tsx b/components/OutcomeChart/SVGLinePattern.tsx new file mode 100644 index 0000000..e6df517 --- /dev/null +++ b/components/OutcomeChart/SVGLinePattern.tsx @@ -0,0 +1,38 @@ +import React, {FunctionComponent} from 'react' + +type SVGLinePatternProps = { + id: string + spacingPx: number + rotationDeg: number + lineWidth?: number + color?: string +} + +const SVGLinePattern: FunctionComponent = props => { + const s = props.spacingPx + 0.5 + return ( + + + + ) +} + +SVGLinePattern.defaultProps = { + lineWidth: 1, + color: '#000' +} + +export default React.memo(SVGLinePattern) diff --git a/components/OutcomeChart/chartColors.ts b/components/OutcomeChart/chartColors.ts new file mode 100644 index 0000000..dc715c9 --- /dev/null +++ b/components/OutcomeChart/chartColors.ts @@ -0,0 +1,11 @@ +export const ChartColors = { + purple: '#6F42C1', + red: '#D73A49', + green: '#28A745', + orange: '#F66A0A', + blue: '#0366D6', + black: '#050505', + pink: '#D03592' +} + +export type ChartColorsType = keyof typeof ChartColors diff --git a/components/ResultTable.module.css b/components/ResultTable.module.css new file mode 100644 index 0000000..944645c --- /dev/null +++ b/components/ResultTable.module.css @@ -0,0 +1,31 @@ +.Title { + @apply p-2; + @apply border-b; + @apply font-medium; + @apply text-sm; +} + +.Row { + @apply flex; + @apply flex-row; + border-bottom: 1px solid #dbdbdb; + @apply font-mono; +} + +.EvenRow { + composes: Row; + background-color: #fbfbfc; +} + +.Label { + @apply p-2; + @apply w-64; +} + +.Value { + composes: Label; + border-color: #dbdbdb; + @apply border-l; + @apply flex-auto; + font-feature-settings: 'tnum'; +} diff --git a/components/ResultTable.tsx b/components/ResultTable.tsx new file mode 100644 index 0000000..f608594 --- /dev/null +++ b/components/ResultTable.tsx @@ -0,0 +1,32 @@ +import classNames from 'classnames' +import numbro from 'numbro' +import React, {FunctionComponent} from 'react' +import styles from './ResultTable.module.css' + +type ResultTableProps = { + title: string + rows: {label: string; value: string | number}[] +} + +const ResultTable: FunctionComponent = ({title, rows}) => { + return ( +
+
{title}
+ {rows.map((r, i) => ( +
+
{r.label}
+
+ {typeof r.value === 'number' + ? numbro(r.value).format({thousandSeparated: true}) + : r.value} +
+
+ ))} +
+ ) +} + +export default ResultTable diff --git a/components/ResultTables.tsx b/components/ResultTables.tsx new file mode 100644 index 0000000..dd3915b --- /dev/null +++ b/components/ResultTables.tsx @@ -0,0 +1,91 @@ +import {DateTime} from 'luxon' +import {cumsum, elementSum, last, maxIndex} from '../lib/arrayMath' +import {ModelOutput} from '../types/model-runner' +import ResultTable from './ResultTable' + +type Props = { + result: ModelOutput +} + +export default function ResultTables(props: Props) { + const {result} = props + const t0 = DateTime.fromISO(result.time.t0, {zone: 'utc'}) + + const peakDate = (arr: number[]) => + t0 + .plus({ + days: result.time.timestamps[maxIndex(arr)] + }) + .toFormat('LLL d, yyyy') + + const estimates = [ + { + label: 'Infected', + value: [ + result.aggregate.metrics.cumMild, + result.aggregate.metrics.cumILI, + result.aggregate.metrics.cumSARI, + result.aggregate.metrics.cumCritical + ] + .map(last) + .reduce((m, v) => m + v, 0) + }, + { + label: 'Hospitalized', + value: [ + result.aggregate.metrics.cumSARI, + result.aggregate.metrics.cumCritical + ] + .map(last) + .reduce((m, i) => m + i) + }, + { + label: 'Require Intensive Care', + value: last(result.aggregate.metrics.cumCritical) + }, + { + label: 'Require Ventilator', + value: Math.ceil(last(result.aggregate.metrics.cumCritical) / 2) + }, + { + label: 'Deaths', + value: last(cumsum(result.aggregate.metrics.incDeath)) + } + ] + + const peaks = [ + { + label: 'Peak Hospital Bed Demand', + value: peakDate( + elementSum([ + result.aggregate.metrics.SARI, + result.aggregate.metrics.Critical, + result.aggregate.metrics.CritRecov + ]) + ) + }, + { + label: 'Peak Intensive Care Demand', + value: peakDate(result.aggregate.metrics.Critical) + }, + { + // vent usage is 50% of total ICU usage according to Silvana (teams chat), + // so just return the same value here. + label: 'Peak Ventilator Demand', + value: peakDate(result.aggregate.metrics.Critical) + }, + { + label: 'Peak Daily Deaths', + value: peakDate(result.aggregate.metrics.incDeath) + } + ] + + return ( +
+
+ +
+ +
+ ) +} diff --git a/components/ResultViewSettings.tsx b/components/ResultViewSettings.tsx new file mode 100644 index 0000000..d8fd1b9 --- /dev/null +++ b/components/ResultViewSettings.tsx @@ -0,0 +1,61 @@ +import {ToggleGroupOption} from './ChartWrapper' +import {ScaleXDomainMonths, ScaleYType} from './OutcomeChart/OutcomeChart' +import selectStyle from './styles/select.module.css' + +type Props = { + disabled: boolean + cumulative: boolean + setCumulative: (isCumulative: boolean) => void + scaleYType: ScaleYType + setScaleYType: (scaleYType: ScaleYType) => void + scaleXDomainMonths: ScaleXDomainMonths + setScaleXDomainMonths: (scaleXDomainMonths: ScaleXDomainMonths) => void + timeToggleOptions: ToggleGroupOption[] +} + +export default function ResultViewSettings(props: Props) { + return ( + <> + + + + + ) +} diff --git a/components/SimulationInputsTable.module.css b/components/SimulationInputsTable.module.css new file mode 100644 index 0000000..29edaa0 --- /dev/null +++ b/components/SimulationInputsTable.module.css @@ -0,0 +1,37 @@ +.h1 { + @apply mt-8 mb-4; + @apply font-bold text-3.25xl; +} + +.h2 { + @apply mt-4; + @apply font-semibold text-lg; +} + +.table td.mild { + @apply bg-severity-mild; + @apply text-severitytext-mild; +} + +.table td.moderate { + @apply bg-severity-moderate; + @apply text-severitytext-moderate; +} + +.table td.aggressive { + @apply bg-severity-aggressive; + @apply text-severitytext-aggressive; +} + +.table td:not(:first-child):not(.socialDistancing) { + @apply text-center; +} + +.Inputs { + @apply flex; +} + +.Inputs .Name { + @apply font-semibold; + @apply pr-3; +} diff --git a/components/SimulationInputsTable.tsx b/components/SimulationInputsTable.tsx new file mode 100644 index 0000000..c06d20c --- /dev/null +++ b/components/SimulationInputsTable.tsx @@ -0,0 +1,80 @@ +import {StrategyDescriptions} from '../lib/new-simulation-state' +import Check from '../svg/Check.svg' +import {InterventionPeriod, ModelInput} from '../types/model-runner' +import LocalDate from './LocalDate' +import styles from './SimulationInputsTable.module.css' +import Table from './Table' + +type Props = { + inputs: ModelInput +} + +export default function SimulationInputsTable(props: Props) { + const inputs = props.inputs + + return ( + <> +

Simulation Inputs

+ + + + + + + {Object.entries(StrategyDescriptions).map(([key, desc]) => ( + + ))} + + + + + + + {inputs.parameters.interventionPeriods.map((pd, i) => ( + + + {Object.keys(StrategyDescriptions).map(strat => { + const intensity = String( + pd[strat as keyof InterventionPeriod] || '' + ) + + return ( + + ) + })} + + + + ))} + +
Starting On + {desc.label} + Contact Reduction
+ + + {strat !== 'socialDistancing' ? ( + intensity ? ( + + ) : null + ) : ( + intensity.charAt(0).toUpperCase() + intensity.slice(1) + )} + {pd.reductionPopulationContact}%
+ +

Other Parameters

+
+
+ R0: +
+
+ {props.inputs.parameters.r0 ?? 'Default'} +
+
+ + ) +} diff --git a/components/SimulationList.module.css b/components/SimulationList.module.css new file mode 100644 index 0000000..ea286b2 --- /dev/null +++ b/components/SimulationList.module.css @@ -0,0 +1,66 @@ +.list { + @apply rounded; + @apply border border-gray-400; + @apply shadow-sm; +} + +.listItem { + @apply border-b; + @apply border-gray-300; + @apply bg-white; + @apply text-sm; +} + +.listItem a { + @apply block; + @apply py-3 px-4; +} + +.listItem:first-child { + @apply rounded-t; +} + +.listItem:last-child { + @apply rounded-b; + @apply border-none; +} + +.listItem .customTitle { + @apply mb-2; + @apply font-bold; +} + +.listItem .region { + @apply block; + @apply mb-2; +} + +.listItem time { + @apply block; + @apply text-gray-600; +} + +.listItem.active { + @apply bg-blue; + @apply text-white; + border-bottom-color: #0356b4; +} + +.listItem.active time { + color: #c8e1ff; +} + +.listItem time svg { + @apply mr-2; + @apply relative; + @apply inline; + bottom: 1px; +} + +.listItem.showMore { + @apply py-3 px-4; + @apply bg-gray-100; + @apply font-bold; + @apply text-gray-800; + @apply cursor-pointer; +} diff --git a/components/SimulationList.tsx b/components/SimulationList.tsx new file mode 100644 index 0000000..44ffecd --- /dev/null +++ b/components/SimulationList.tsx @@ -0,0 +1,80 @@ +import {AxiosError} from 'axios' +import {DateTime} from 'luxon' +import Link from 'next/link' +import {useState} from 'react' +import useSWR from 'swr' +import {SimulationSummary} from '../lib/db' +import flagAndName from '../lib/regionEmoji' +import Clock from '../svg/Clock.svg' +import simListStyle from './SimulationList.module.css' + +type Props = { + activeSimulationID: number + initialData: SimulationSummary[] +} + +export default function SimulationList(props: Props) { + const {data, error} = useSWR( + '/api/simulations', + { + initialData: props.initialData, + shouldRetryOnError: true, + refreshInterval: 30_000 + } + ) + + const [summaryCount, setSummaryCount] = useState(5) + const hasMore = data && summaryCount < data.length + + if (error) { + return

Error loading simulation list.

+ } + + if (!data) { + return

Loading simulation summaries...

+ } + + return ( + + ) +} + +function getRelativeTime(dateTime: string) { + // https://github.com/moment/luxon/issues/478 + const dt = DateTime.fromISO(dateTime).toRelative() + return dt === 'in 0 seconds' ? 'Just now' : dt +} diff --git a/components/StatusBlock.module.css b/components/StatusBlock.module.css new file mode 100644 index 0000000..715827a --- /dev/null +++ b/components/StatusBlock.module.css @@ -0,0 +1,8 @@ +.loadingBlock { + @apply border; + @apply rounded; + @apply flex flex-col items-center justify-center; + @apply shadow-sm; + min-height: 375px; + background-image: linear-gradient(180deg, #ffffff 0%, #fbfbfc 100%); +} diff --git a/components/StatusBlock.tsx b/components/StatusBlock.tsx new file mode 100644 index 0000000..71a17cd --- /dev/null +++ b/components/StatusBlock.tsx @@ -0,0 +1,18 @@ +import {PropsWithChildren} from 'react' +import styles from './StatusBlock.module.css' +import StatusIcon from './StatusIcon' + +type Props = { + statusKey: string +} + +export default function StatusBlock(props: PropsWithChildren) { + return ( +
+
+ +
+
{props.children}
+
+ ) +} diff --git a/components/StatusIcon.module.css b/components/StatusIcon.module.css new file mode 100644 index 0000000..76aea00 --- /dev/null +++ b/components/StatusIcon.module.css @@ -0,0 +1,12 @@ +.svg-rotate { + animation: infinite-rotate 2s linear infinite; +} + +@keyframes infinite-rotate { + 0% { + transform: rotate(0deg); + } + 100% { + transform: rotate(360deg); + } +} diff --git a/components/StatusIcon.tsx b/components/StatusIcon.tsx new file mode 100644 index 0000000..63a10d7 --- /dev/null +++ b/components/StatusIcon.tsx @@ -0,0 +1,41 @@ +import Dot from '../svg/Dot.svg' +import Failure from '../svg/Failure.svg' +import StatusSpinner from '../svg/StatusSpinner.svg' +import Success from '../svg/Success.svg' +import styles from './StatusIcon.module.css' + +interface Props { + statusKey: string +} + +export default function StatusIcon(props: Props) { + switch (props.statusKey) { + case 'pending': + return ( +
+ +
+ ) + case 'in-progress': + return ( +
+ +
+ ) + case 'failed': + return ( +
+ +
+ ) + case 'complete': + return ( +
+ +
+ ) + default: + // no icon + return
+ } +} diff --git a/components/Table.module.css b/components/Table.module.css new file mode 100644 index 0000000..dbf9624 --- /dev/null +++ b/components/Table.module.css @@ -0,0 +1,60 @@ +.table { + @apply w-full; + @apply rounded; + @apply border-separate; + @apply bg-white; + @apply shadow-sm; + @apply text-left text-sm; +} + +.table.fixed { + @apply table-fixed; +} + +.table.auto { + @apply table-auto; +} + +.table th, +.table td { + @apply p-3; +} + +.table th { + @apply border; + @apply font-semibold; + border-right: none; + border-bottom-color: black; +} + +.table th:first-child { + @apply rounded-tl; +} + +.table th:last-child { + @apply border-r; + @apply rounded-tr; + border-right: 1px solid #e0e0e0; +} + +.table td { + @apply font-mono; + @apply border-b border-l; + border-top: none; +} + +.table td:not(:first-child) { + border-color: rgba(0, 0, 0, 0.16); +} + +.table td:last-child { + border-right-width: 1px; +} + +.table tr:last-child td:first-child { + @apply rounded-bl; +} + +.table tr:last-child td:last-child { + @apply rounded-br; +} diff --git a/components/Table.tsx b/components/Table.tsx new file mode 100644 index 0000000..94d0448 --- /dev/null +++ b/components/Table.tsx @@ -0,0 +1,19 @@ +import styles from './Table.module.css' + +type Props = JSX.IntrinsicElements['table'] & { + fixed?: boolean +} + +export default function Table(props: Props) { + const layout = props.fixed ? 'fixed' : 'auto' + + return ( + + {props.children} +
+ ) +} diff --git a/components/simulation-form/ApplicationComponent.module.css b/components/simulation-form/ApplicationComponent.module.css new file mode 100644 index 0000000..0832fb9 --- /dev/null +++ b/components/simulation-form/ApplicationComponent.module.css @@ -0,0 +1,17 @@ +.Content { + @apply flex-1; + @apply p-3; + @apply rounded; + + background-color: #f7f7f9; + border: 1px solid #e2e8f0; +} + +.Heading h3 { + @apply font-semibold; +} + +.Heading p, +.Content p { + color: #52555F; +} diff --git a/components/simulation-form/ApplicationComponent.tsx b/components/simulation-form/ApplicationComponent.tsx new file mode 100644 index 0000000..a0bdc10 --- /dev/null +++ b/components/simulation-form/ApplicationComponent.tsx @@ -0,0 +1,14 @@ +import {PropsWithChildren} from 'react' +import styles from './ApplicationComponent.module.css' + +export default function ApplicationComponent(props: PropsWithChildren<{}>) { + return ( +
+
+

Continuous application

+

Strategy is enforced for a specific period of time.

+
+ {props.children} +
+ ) +} diff --git a/components/simulation-form/DateInput.tsx b/components/simulation-form/DateInput.tsx new file mode 100644 index 0000000..17bdc1e --- /dev/null +++ b/components/simulation-form/DateInput.tsx @@ -0,0 +1,59 @@ +import {CleaveOptions} from 'cleave.js/options' +import Cleave from 'cleave.js/react' +import {useMemo, useState} from 'react' +import {isValidDate, toYYYYMMDD} from '../../lib/dateFunctions' +import formStyle from '../styles/form.module.css' + +interface Props { + value: string | Date + max?: string | Date + min?: string | Date + onChange?: (newDate: string) => void +} + +/** + * A component that displays a platform native date picker + * and allows a user to choose a date within a given range. + * + * Dates are expected and returned in yyyy-mm-dd format. + * + */ +export default function DateInput(props: Props): JSX.Element { + const [error, setError] = useState(false) + const value: string = useMemo( + () => (props.value instanceof Date ? toYYYYMMDD(props.value) : props.value), + [props.value] + ) + const min: string | undefined = useMemo( + () => (props.min instanceof Date ? toYYYYMMDD(props.min) : props.min), + [props.min] + ) + const max: string | undefined = useMemo( + () => (props.max instanceof Date ? toYYYYMMDD(props.max) : props.max), + [props.max] + ) + return ( + { + props.onChange && props.onChange(e.target.value) + setError(!isValidDate(e.target.value)) + }} + options={ + { + date: true, + datePattern: ['Y', 'm', 'd'], + delimiters: ['-'], + dateMin: min, + dateMax: max + } as CleaveOptions // DefinitelyTyped def is out of date + } + /> + ) +} diff --git a/components/simulation-form/ErrorMessage.tsx b/components/simulation-form/ErrorMessage.tsx new file mode 100644 index 0000000..b5f83fc --- /dev/null +++ b/components/simulation-form/ErrorMessage.tsx @@ -0,0 +1,80 @@ +import Joi from '@hapi/joi' +import isEqual from 'lodash/isEqual' +import boxStyle from '../styles/box.module.css' + +type Path = Joi.ValidationErrorItem['path'] + +type Props = { + error: Joi.ValidationError | null + path: Path + children: (errors: Joi.ValidationErrorItem[]) => JSX.Element +} + +/** + * Render the children once per error if there's an error for the given path on the validation + * error. + * + * {details => ( + *
    {details.map((d, i) =>
  • {d.message}
    • )}
+ * )} + */ +export default function ErrorMessage(props: Props) { + const details = props.error?.details ?? [] + const relevantErrors = getRelevantErrors(details, props.path) + + if (!relevantErrors.length) { + return null + } + + return props.children(relevantErrors) +} + +export function ErrorList( + props: Omit & {className?: string} +) { + return ( + + {details => ( +
    + {details.map((d, i) => ( +
  • {d.message}
    • + ))} +
+ )} + + ) +} + +/** + * A helper to get a CSS class when an error exists for a given path + * + * @param error The validation error (or null) + * @param path The path to check errors at + * @param ifError The value to return if at least one error is present + */ +export function errorClass( + error: Joi.ValidationError | null, + path: Path, + ifError: string +): string { + const details = error?.details ?? [] + + if (getRelevantErrors(details, path).length > 0) { + return ifError + } + + return '' +} + +function getRelevantErrors( + details: Joi.ValidationErrorItem[], + path: Path +): Joi.ValidationErrorItem[] { + return details.reduce((errors, detail) => { + if (isEqual(detail.path, path)) { + errors.push(detail) + } + + return errors + }, []) +} diff --git a/components/simulation-form/FormSection.module.css b/components/simulation-form/FormSection.module.css new file mode 100644 index 0000000..7c066fe --- /dev/null +++ b/components/simulation-form/FormSection.module.css @@ -0,0 +1,29 @@ +.FormSection { + @apply mb-4; + @apply p-4; + @apply rounded; + @apply border; + @apply bg-white; + @apply shadow-sm; + @apply text-sm; + border-color: rgba(65, 67, 78, 0.25); +} + +.FormSectionHeader { + @apply pb-4; +} + +.FormSectionHeader h2 { + @apply font-semibold; + @apply text-base; +} + +.FormSectionHeader p { + @apply mt-2; + @apply text-light-gray; +} + +.FormSectionError { + background-color: #ffeef0; + border-color: #f97583; +} diff --git a/components/simulation-form/FormSection.tsx b/components/simulation-form/FormSection.tsx new file mode 100644 index 0000000..b285908 --- /dev/null +++ b/components/simulation-form/FormSection.tsx @@ -0,0 +1,29 @@ +import {PropsWithChildren} from 'react' +import styles from './FormSection.module.css' + +type Props = { + title?: string + description?: string + isError?: boolean +} + +export default function FormSection(props: PropsWithChildren) { + return ( +
+ {props.title && ( +
+ {props.title &&

{props.title}

} + {props.description &&

{props.description}

} +
+ )} + + {props.children} +
+ ) +} diff --git a/components/simulation-form/Important.module.css b/components/simulation-form/Important.module.css new file mode 100644 index 0000000..51f7c4f --- /dev/null +++ b/components/simulation-form/Important.module.css @@ -0,0 +1,6 @@ +.Important { + @apply pl-2; + @apply my-2; + + border-left: solid red 4px; +} diff --git a/components/simulation-form/Important.tsx b/components/simulation-form/Important.tsx new file mode 100644 index 0000000..8d2b973 --- /dev/null +++ b/components/simulation-form/Important.tsx @@ -0,0 +1,6 @@ +import {PropsWithChildren} from 'react' +import styles from './Important.module.css' + +export default function Important(props: PropsWithChildren<{}>): JSX.Element { + return

{props.children}

+} diff --git a/components/simulation-form/InterventionGuidanceLink.module.css b/components/simulation-form/InterventionGuidanceLink.module.css new file mode 100644 index 0000000..4935150 --- /dev/null +++ b/components/simulation-form/InterventionGuidanceLink.module.css @@ -0,0 +1,22 @@ +.link { + @apply flex; + @apply items-center justify-center; + @apply rounded; + @apply mt-2; + @apply p-3; + + background-color: #f7f7f9; +} + +.link .logo { + width: 16px; +} + +.link .text { + @apply flex-1; + @apply m-0 p-0 ml-3; +} + +.link .chevron { + @apply transform -rotate-90; +} diff --git a/components/simulation-form/InterventionGuidanceLink.tsx b/components/simulation-form/InterventionGuidanceLink.tsx new file mode 100644 index 0000000..5b1fe66 --- /dev/null +++ b/components/simulation-form/InterventionGuidanceLink.tsx @@ -0,0 +1,19 @@ +import Chevron from '../../svg/Chevron.svg' +import OutboundLink from '../OutboundLink' +import styles from './InterventionGuidanceLink.module.css' + +type Props = { + logo: JSX.Element + href: string + text: string +} + +export default function InterventionGuidanceLink(props: Props) { + return ( + +
{props.logo}
+

{props.text}

+ + + ) +} diff --git a/components/simulation-form/InterventionPeriodSection.module.css b/components/simulation-form/InterventionPeriodSection.module.css new file mode 100644 index 0000000..5b729f2 --- /dev/null +++ b/components/simulation-form/InterventionPeriodSection.module.css @@ -0,0 +1,106 @@ +.InterventionPeriodSection { + position: relative; +} + +.AutoGenMessage { + @apply p-4; + @apply flex; + background-color: #f1f8ff; +} + +.AutoGenMessage div { + @apply text-xs; + @apply m-0; +} + +.AutoGenMessage svg { + @apply mr-2; + width: 2rem; +} + +.StrategyList, +.StrategyList > li, +.Intensity { + border-color: #ccc; +} + +.StrategyList { + @apply rounded; + @apply border; + @apply shadow-sm; + background-image: linear-gradient(180deg, #ffffff 0%, #fbfbfc 100%); +} + +.StrategyList > li { + @apply border-b; +} + +.StrategyList > li:last-child { + @apply border-none; +} + +.Strategy, +.Intensity { + @apply w-full flex; + @apply p-4 pb-2; +} + +.Intensity { + @apply pl-8; + @apply border-t; + @apply text-gray-800; +} + +.Strategy input, +.Intensity input { + @apply mr-3; +} + +.Strategy label, +.Intensity label { + position: relative; + bottom: 0.25rem; +} + +.Intensities { + background-color: #f7f7f9; +} + +.RemoveButton { + @apply bg-white; + color: #cb2431; + position: absolute; + top: 1.3rem; + right: 1.3rem; +} + +.PercInput { + @apply flex; +} + +.PercInput input { + border-top-right-radius: 0; + border-bottom-right-radius: 0; +} + +.PercInput .PercSign { + @apply border-t border-r border-b; + @apply rounded-r; + @apply px-4 py-3; + background-image: linear-gradient(180deg, #ffffff 0%, #fbfbfc 100%); +} + +.PercInput .PercSign.warn { + @apply border-orange; + @apply bg-orange; + opacity: 50; + color: #a04100; + background-color: #ffebda; + background-image: none; +} + +.InterventionPeriodSection h3 { + @apply mb-3; + @apply mt-6; + @apply font-semibold; +} diff --git a/components/simulation-form/InterventionPeriodSection.tsx b/components/simulation-form/InterventionPeriodSection.tsx new file mode 100644 index 0000000..7a49fea --- /dev/null +++ b/components/simulation-form/InterventionPeriodSection.tsx @@ -0,0 +1,242 @@ +import Joi from '@hapi/joi' +import {useMemo} from 'react' +import {SupportedParameter} from '../../lib/models' +import { + Intensity, + InterventionPeriod, + StrategyDescriptions, + StrategyKey +} from '../../lib/new-simulation-state' +import Descartes from '../../svg/Descartes.svg' +import SocialDistancingGraphic from '../../svg/SocialDistancingGraphic.svg' +import Trash from '../../svg/Trash.svg' +import Unacast from '../../svg/Unacast.svg' +import Warn from '../../svg/Warn.svg' +import {ISODate} from '../../types/model-runner' +import formStyle from '../styles/form.module.css' +import DateInput from './DateInput' +import {ErrorList} from './ErrorMessage' +import FormSection from './FormSection' +import InterventionGuidanceLink from './InterventionGuidanceLink' +import styles from './InterventionPeriodSection.module.css' +import {SupportedParameters} from './SupportedParameters' + +interface Props { + period: InterventionPeriod + isFirst: boolean + onChange: (config: Partial) => void + onChangeIntervention: (update: Pick) => void + remove: () => void + priorPeriodStartDate: ISODate | undefined + error: Joi.ValidationError | null + index: number +} + +const autoGeneratedPeriodText = `This intervention start date and policy settings were populated +based on the latest known real-world data. You may modify this to run +simulations, or correct this data by editing below.` + +function enforceBounds(strNumber: number | string): number | '' { + const num = + typeof strNumber === 'number' ? strNumber : parseInt(strNumber, 10) + return Number.isNaN(num) ? '' : num < 0 ? 0 : num > 100 ? 100 : num +} + +// TODO Need to constrain the start date of the period to ensure it fits within the range +export default function InterventionPeriodSection(props: Props) { + const contactReduction = enforceBounds( + props.period.reductionPopulationContact + ) + return ( +
+ + {!props.isFirst && ( + + )} + {props.period.isAutoGenerated && ( +
+ +
{autoGeneratedPeriodText}
+
+ )} + {props.isFirst ? ( +

Intervention policies started on

+ ) : ( +

Starting on

+ )} + + props.onChange({ + startDate + }) + } + /> + + + +

+ Intervention strategies{' '} + +

+ +
    + {Object.entries(StrategyDescriptions).map( + ([strategyKey, description]) => ( + + props.onChangeIntervention({ + [strategyKey]: enabled ? intensity : undefined + }) + } + /> + ) + )} +
+ +

+ Contact reduction{' '} + +

+

+ Based on the intervention strategies selected above, what is the + estimated reduction in population contact? +

+
+ { + const reductionPopulationContact = enforceBounds(e.target.value) + props.onChange({reductionPopulationContact}) + }} + /> +
+ % +
+
+ + + +

+ +

+

+ Estimating this reduction is not an exact science. It is recommended + to familiarize yourself with the latest contact reduction rates from + the following data sources: +

+ + } + href="https://www.google.com/covid19/mobility/" + text="Google’s COVID-19 Community Mobility Reports" + /> + + } + href="https://www.descarteslabs.com/mobility/" + text="Descartes Labs - Changes in US Mobility Report" + /> + + } + href="https://www.unacast.com/covid19/social-distancing-scoreboard" + text="Unacast Social Distancing Scoreboard" + /> + +
+ ) +} + +interface StrategyProps { + enabled: boolean + label: string + descriptions?: Record + intensity: Intensity + onChange: (enabled: boolean, intensity: Intensity) => void +} + +function Strategy(props: StrategyProps) { + const randomID = () => + Math.random() + .toString(36) + .substring(2, 15) + + const idBase = useMemo(() => `${randomID()}${randomID()}`, []) + + return ( +
  • +
    + props.onChange(e.target.checked, props.intensity)} + /> + +
    + {props.descriptions && props.enabled && ( +
      + {Object.entries(Intensity).map(([label, intensity]) => ( +
    • + props.onChange(true, intensity)} + /> + +
      • + ))} +
    + )} +
    • + ) +} diff --git a/components/simulation-form/NewSimulationForm.module.css b/components/simulation-form/NewSimulationForm.module.css new file mode 100644 index 0000000..a60e237 --- /dev/null +++ b/components/simulation-form/NewSimulationForm.module.css @@ -0,0 +1,31 @@ +.NewSimulationForm { + @apply mx-auto; + margin-top: 49px; + max-width: 595px; +} + +.NewSimulationForm h1 { + @apply mt-2 mb-14; + @apply font-bold; + @apply text-2xl; +} + +.SimulationLabel { + @apply border; + @apply rounded; + @apply text-black; + @apply py-3 px-4; + @apply my-2; + + border-color: #cccccc; + width: 100%; + text-align: left; +} + +.NewSimulationForm p { + @apply mt-4 mb-2; +} + +.ButtonMessage { + @apply px-2; +} diff --git a/components/simulation-form/NewSimulationForm.tsx b/components/simulation-form/NewSimulationForm.tsx new file mode 100644 index 0000000..0c9f365 --- /dev/null +++ b/components/simulation-form/NewSimulationForm.tsx @@ -0,0 +1,367 @@ +import Joi from '@hapi/joi' +import Link from 'next/link' +import {useRouter} from 'next/router' +import {useContext, useMemo, useReducer, useState} from 'react' +import {cache} from 'swr' +import useAbort from '../../hooks/use-abort' +import {SupportedParameter} from '../../lib/models' +import { + createFormBody, + getInterventionsEnd, + getNextInterventionPeriodStart, + initializeSimulationState, + InterventionPeriod, + reducer, + StrategyKey, + validateSchema +} from '../../lib/new-simulation-state' +import flagAndName from '../../lib/regionEmoji' +import {InterventionMap} from '../../lib/simulation-types' +import {SentryContext} from '../../pages/_app' +import Plus from '../../svg/Plus.svg' +import {Region, RegionMap, TopLevelRegion} from '../../types/regions' +import btnStyles from '../styles/button.module.css' +import formStyle from '../styles/form.module.css' +import selectStyles from '../styles/select.module.css' +import {errorClass, ErrorList} from './ErrorMessage' +import FormSection from './FormSection' +import InterventionPeriodSection from './InterventionPeriodSection' +import styles from './NewSimulationForm.module.css' +import {SupportedParameters} from './SupportedParameters' + +interface Props { + regions: RegionMap + interventions: InterventionMap +} + +export default function NewSimulationForm(props: Props) { + const {captureException} = useContext(SentryContext) + const initialRegion = useMemo( + () => ({ + region: props.regions.US, + subregion: Object.values(props.regions.US.regions)[0] + }), + [props.regions] + ) + const [disableSubmit, setDisableSubmit] = useState(false) + const [showingAdvanced, setShowingAdvanced] = useState(false) + + const [state, dispatch] = useReducer( + reducer, + initializeSimulationState(initialRegion, props.interventions) + ) + const abortSignal = useAbort() + const router = useRouter() + const [errorMsg, setErrorMsg] = useState() + const [ + validationError, + setValidationError + ] = useState(null) + + const setRegion = (region: TopLevelRegion) => + dispatch({type: 'SET_REGION', region, interventions: props.interventions}) + const setSubregion = (subregion: Region) => + dispatch({ + type: 'SET_SUBREGION', + subregion, + interventions: props.interventions + }) + const setLabel = (label: string) => dispatch({type: 'SET_LABEL', label}) + const setR0 = (r0: number | undefined) => dispatch({type: 'SET_R0', r0}) + const updatePeriod = ( + period: InterventionPeriod, + newPeriod: Partial + ) => dispatch({type: 'UPDATE_PERIOD', period, newPeriod}) + const updatePeriodIntervention = ( + period: InterventionPeriod, + update: Pick + ) => dispatch({type: 'UPDATE_PERIOD_INTERVENTIONS', period, update}) + const removePeriod = (period: InterventionPeriod) => + dispatch({type: 'REMOVE_PERIOD', period}) + + const addInterventionPeriod = () => + dispatch({ + type: 'ADD_PERIOD', + period: { + ...state.interventionPeriods[state.interventionPeriods.length - 1], + reductionPopulationContact: '', + startDate: getNextInterventionPeriodStart(state.interventionPeriods), + isAutoGenerated: false + } + }) + + const addInterventionPeriodEnd = () => + dispatch({ + type: 'ADD_PERIOD', + period: { + startDate: getInterventionsEnd(state.interventionPeriods), + isAutoGenerated: false, + reductionPopulationContact: 0 + } + }) + + const topLevelregions = useMemo( + () => + Object.values(props.regions).sort((r1, r2) => + r1.name.localeCompare(r2.name) + ), + [props.regions] + ) + + const subregions = useMemo( + () => + Object.values(state.region.regions).sort((r1, r2) => + r1.name.localeCompare(r2.name) + ), + [state.region.regions] + ) + + const handleValidationError = (err: Joi.ValidationError | null) => { + if (!err) { + setValidationError(null) + setErrorMsg('') + return + } + + setValidationError(err) + setErrorMsg('Please correct the errors in the form above.') + } + + const onSubmit = async () => { + try { + setDisableSubmit(true) + handleValidationError(null) + const input = createFormBody(state) + const error = validateSchema(input) + + if (error) { + throw error + } + + const res = await fetch('/api/simulations', { + method: 'POST', + signal: abortSignal, + body: JSON.stringify(input) + }) + + if (res.status === 200) { + const {id}: {id: number} = await res.json() + cache.delete('/api/simulations') + router.push('/simulations/[id]', `/simulations/${id}`) + window.scrollTo(0, 0) + } else { + const error = await res.json() + throw new Error(error.error) + } + } catch (err) { + console.error(err) + if (err.name === 'ValidationError') { + handleValidationError(err) + } else { + setErrorMsg(err.message) + captureException(err) + } + } finally { + setDisableSubmit(false) + } + } + + const hasSubregions = + Object.keys(state.region.regions).length > 1 || + Object.keys(state.region.regions)[0] !== '_self' + + return ( +
    e.preventDefault()} + > + + ← Return to simulation list + + +

    Create Simulation

    + + +

    + Choose a region and subregion for this simulation. Simulations will + provide more accurate results as the location becomes more specific. +

    +
    + +
    + {hasSubregions ? ( +
    + +
    + ) : null} +     + + +

    + Add a memorable name to make this simulation easier to find in the + future. +

    + { + setLabel(e.target.value) + }} + /> + + +     + + {state.interventionPeriods.map((period, i) => ( + ) => + updatePeriod(period, newPeriod) + } + onChangeIntervention={( + update: Pick + ) => updatePeriodIntervention(period, update)} + remove={() => removePeriod(period)} + /> + ))} + +
    + + +
    + + + setShowingAdvanced(!showingAdvanced)} + className="cursor-pointer font-semibold" + > + {showingAdvanced ? 'Hide' : 'View'} advanced controls + + + {showingAdvanced && ( +
    +

    + + +

    + +
    + { + setR0(Number(e.target.value) || undefined) + }} + onBlur={e => + (e.target.value = + typeof state.r0 === 'number' ? state.r0.toFixed(1) : '') + } + /> +
    + +

    + The estimated number of new infections that will be caused for + each existing infection. Leave this field blank to let each model + decide its own R0. +

    +
    + )} +     + + {errorMsg && ( + + {validationError && ( +
      + {validationError.details.map((d, i) => ( +
    • + {d.message} +
      • + ))} +
    + )} + +

    {errorMsg}

    +     + )} + +
    + +
    + + ) +} diff --git a/components/simulation-form/RangeInput.module.css b/components/simulation-form/RangeInput.module.css new file mode 100644 index 0000000..fe4820c --- /dev/null +++ b/components/simulation-form/RangeInput.module.css @@ -0,0 +1,19 @@ +.RangeInput { + @apply flex; +} + +.RangeInput input[type='number'] { + @apply mr-4; + @apply pl-5 py-3; + @apply border; + @apply rounded; + border-color: #cccccc; +} + +.RangeInput input[type='number']:focus { + @apply outline-none; +} + +.RangeInput input[type='range'] { + @apply flex-grow; +} diff --git a/components/simulation-form/RangeInput.tsx b/components/simulation-form/RangeInput.tsx new file mode 100644 index 0000000..2c0e323 --- /dev/null +++ b/components/simulation-form/RangeInput.tsx @@ -0,0 +1,66 @@ +import styles from './RangeInput.module.css' + +type Props = { + value: number + min: number + max: number + disabled?: boolean + onChange: (value: number) => void +} + +export default function RangeInput(props: Props) { + // handle the case where the min/max has changed + if (props.value < props.min) { + props.onChange(props.min) + } + if (props.value > props.max) { + props.onChange(props.max) + } + + return ( +
    + { + const value = parseValue(e.target.value, props.min, props.max) + props.onChange(value) + }} + /> + { + const value = parseValue(e.target.value, props.min, props.max) + props.onChange(value) + }} + /> +
    + ) +} + +function parseValue(value: string, min: number, max: number): number { + const parsed = parseInt(value, 10) + + if (isNaN(parsed)) { + return min + } + + if (parsed < min) { + return min + } + + if (parsed > max) { + return max + } + + return parsed +} diff --git a/components/simulation-form/StrategyConfiguration.module.css b/components/simulation-form/StrategyConfiguration.module.css new file mode 100644 index 0000000..be8d6bd --- /dev/null +++ b/components/simulation-form/StrategyConfiguration.module.css @@ -0,0 +1,52 @@ +.StrategyConfigurationParam { + @apply flex-1; + @apply mr-4; + @apply mt-4; +} + +.ConfigurableInput { + @apply flex; + @apply items-start; + @apply text-sm; +} + +.ConfigurableInput + .ConfigurableInput { + @apply pt-3; +} + +.ConfigurableInputSubsection { + @apply flex; + @apply items-start; + @apply text-sm; + @apply pt-1; + @apply w-full; + padding-left: 1.3rem; +} + +.ConfigurableInputSubsection + .ConfigurableInputSubsection { + @apply pl-10; +} + +.Content { + @apply flex-1; + @apply ml-3; +} + +.Heading h3 { + @apply font-semibold; + @apply text-lg; +} + +/* Nested Configurable elements have a smaller header */ +.ConfigurableInputSubsection .ConfigurableInput .Heading h3 { + @apply text-base; +} + +.ConfigurableInputSubsection .ConfigurableInput .Heading p { + @apply text-sm; +} + +.ConfigurableInput p { + @apply text-base; + color: #52555f; +} diff --git a/components/simulation-form/SupportedParameters.module.css b/components/simulation-form/SupportedParameters.module.css new file mode 100644 index 0000000..e2d3587 --- /dev/null +++ b/components/simulation-form/SupportedParameters.module.css @@ -0,0 +1,76 @@ +.SupportedParameters { + @apply inline; + @apply relative; + @apply ml-3; + @apply mr-10; + + top: 0.25rem; + z-index: 1; +} + +.UsedByButton { + @apply inline-flex; + @apply text-xxs; + @apply bg-gray-lightest; + @apply rounded-full; + @apply px-3 py-1; +} + +.UsedByButton:focus { + outline: none; +} + +.UsedByButton svg { + @apply mr-2; + + width: 16px; + height: 16px; +} + +.PopUp { + @apply border border-solid rounded; + @apply absolute; + @apply bg-white; + @apply p-2; + + box-shadow: 0 1px 3px 0 rgba(0, 0, 0, 0.5); + left: -3.9rem; + top: 25px; +} + +.PopUp:before { + content: ' '; + top: -6px; + left: 77px; + height: 8px; + width: 8px; + + border: 2px solid #e0e0e0; + border-right: none; + border-top: none; + background: white; + position: absolute; + pointer-events: none; + transform: rotate(135deg); +} + +.Hidden { + display: none; +} + +.PopUp h4 { + @apply font-semibold; + + text-align: left; +} + +.PopUp li { + @apply my-2; + + text-align: left; + display: flex; +} + +.PopUp li svg { + color: green; +} diff --git a/components/simulation-form/SupportedParameters.tsx b/components/simulation-form/SupportedParameters.tsx new file mode 100644 index 0000000..1e7a549 --- /dev/null +++ b/components/simulation-form/SupportedParameters.tsx @@ -0,0 +1,59 @@ +import {useState} from 'react' +import models, { + SupportedParameter, + supportedParameterDesc +} from '../../lib/models' +import Check from '../../svg/Check.svg' +import Info from '../../svg/Info.svg' +import styles from './SupportedParameters.module.css' + +interface Props { + parameterId: SupportedParameter +} + +export function SupportedParameters(props: Props) { + const [show, setShow] = useState(false) + const [stickyShow, setStickyShow] = useState(false) + + return ( +
    + +
    + ) +} + +function getUsedByCount(parameterId: SupportedParameter) { + return Object.values(models).reduce( + (cnt, model) => + model.supportedParameters.includes(parameterId) ? cnt + 1 : cnt, + 0 + ) +} + +function getUsedByNames(parameterId: SupportedParameter): JSX.Element[] { + return Object.values(models) + .filter(model => model.supportedParameters.includes(parameterId)) + .map(model => ( +
  • + + {model.name} +
    • + )) +} diff --git a/components/styles/box.module.css b/components/styles/box.module.css new file mode 100644 index 0000000..874e9a4 --- /dev/null +++ b/components/styles/box.module.css @@ -0,0 +1,15 @@ +.box { + @apply mb-4; + @apply p-4; + @apply rounded; + @apply border; + @apply bg-white; + @apply shadow-sm; + @apply text-sm; + border-color: rgba(65, 67, 78, 0.25); +} + +.box.error { + background-color: #ffeef0; + border-color: #f97583; +} diff --git a/components/styles/button.module.css b/components/styles/button.module.css new file mode 100644 index 0000000..13268ae --- /dev/null +++ b/components/styles/button.module.css @@ -0,0 +1,25 @@ +.button { + @apply px-4 py-3; + @apply rounded; + @apply border border-gray-400; + @apply text-sm; + @apply shadow-sm; + @apply bg-white; + @apply text-center; +} + +.button:focus { + @apply outline-none; +} + +.button.orange { + @apply bg-orange-300; + @apply text-white; + @apply border-none; +} + +.button.blue { + @apply bg-blue; + @apply text-white; + @apply border-none; +} diff --git a/components/styles/form.module.css b/components/styles/form.module.css new file mode 100644 index 0000000..8b1b1eb --- /dev/null +++ b/components/styles/form.module.css @@ -0,0 +1,26 @@ +.textInput { + @apply rounded; + @apply py-3 px-4; + border: 1px solid rgba(0, 0, 0, 0.16); + background-color: #fbfbfc; + box-shadow: inset 0px 1px 2px rgba(0, 0, 0, 0.12); +} + +.textInput:focus { + @apply outline-none; + @apply shadow-outline; +} + +.textInput.error { + @apply border border-red; +} + +.textInput.warn { + @apply border border-orange; + color: #A04100; + background-color: #FFF8F2; +} + +.textInput.warn::placeholder { + color: #A04100; +} diff --git a/components/styles/select.module.css b/components/styles/select.module.css new file mode 100644 index 0000000..8fbfbdf --- /dev/null +++ b/components/styles/select.module.css @@ -0,0 +1,36 @@ +.select { + @apply pl-4 pr-8 py-3; + @apply appearance-none; + @apply border border-gray-400; + @apply border-gray-300; + @apply bg-white; + @apply rounded; + @apply outline-none; + @apply shadow-sm; + + background-image: url('../../svg/Chevron.svg'), + linear-gradient(180deg, #ffffff 0%, #fbfbfc 100%); + background-repeat: no-repeat, repeat; + background-position: right 0.75rem center, top left; +} + +.selectGroup { + @apply rounded; + @apply border border-gray-400; + @apply shadow-sm; +} + +.selectGroup .select { + @apply border-none border-b; + @apply rounded-none; + @apply shadow-none; +} + +.selectGroup .select:first-child { + @apply rounded-t; +} + +.selectGroup .select:last-child { + @apply rounded-b; + @apply border-none; +} diff --git a/components/table/TableHeader.tsx b/components/table/TableHeader.tsx new file mode 100644 index 0000000..e2c2ffb --- /dev/null +++ b/components/table/TableHeader.tsx @@ -0,0 +1,12 @@ +import {SortIndicator, TableHeaderProps} from 'react-virtualized' + +export default function TableHeader(props: TableHeaderProps) { + return ( + <> + {props.label} + {props.sortBy === props.dataKey && ( + + )} + + ) +} diff --git a/css/app.css b/css/app.css new file mode 100644 index 0000000..f326031 --- /dev/null +++ b/css/app.css @@ -0,0 +1,11 @@ +/* purgecss start ignore */ +@import url('https://fonts.googleapis.com/css2?family=Anonymous+Pro&display=swap'); +@tailwind base; +@tailwind components; +/* purgecss end ignore */ + +@tailwind utilities; + +body { + @apply bg-gray; +} diff --git a/data/hospitals/us.json b/data/hospitals/us.json new file mode 100644 index 0000000..1d7cfff --- /dev/null +++ b/data/hospitals/us.json @@ -0,0 +1,563 @@ +[ + { + "id": 1, + "name": "Alaska", + "abbr": "AK", + "population": 731545, + "licensed_beds": 1760, + "total_beds": 1542, + "icu_beds": 106, + "utilization": 0.380437458, + "pct_icu": 6.87 + }, + { + "id": 2, + "name": "Alabama", + "abbr": "AL", + "population": 4903185, + "licensed_beds": 18667, + "total_beds": 14974, + "icu_beds": 1105, + "utilization": 0.47099424, + "pct_icu": 7.38 + }, + { + "id": 3, + "name": "Arkansas", + "abbr": "AR", + "population": 3017825, + "licensed_beds": 12869, + "total_beds": 9990, + "icu_beds": 667, + "utilization": 0.435393057, + "pct_icu": 6.68 + }, + { + "id": 4, + "name": "Arizona", + "abbr": "AZ", + "population": 7278717, + "licensed_beds": 17163, + "total_beds": 15379, + "icu_beds": 1263, + "utilization": 0.514369816, + "pct_icu": 8.21 + }, + { + "id": 5, + "name": "California", + "abbr": "CA", + "population": 39512223, + "licensed_beds": 85161, + "total_beds": 80802, + "icu_beds": 6925, + "utilization": 0.54043979, + "pct_icu": 8.57 + }, + { + "id": 6, + "name": "Colorado", + "abbr": "CO", + "population": 5758736, + "licensed_beds": 12955, + "total_beds": 10659, + "icu_beds": 962, + "utilization": 0.465875256, + "pct_icu": 9.03 + }, + { + "id": 7, + "name": "Connecticut", + "abbr": "CT", + "population": 3565287, + "licensed_beds": 8185, + "total_beds": 8047, + "icu_beds": 572, + "utilization": 0.608170065, + "pct_icu": 7.11 + }, + { + "id": 8, + "name": "Delaware", + "abbr": "DE", + "population": 973764, + "licensed_beds": 3034, + "total_beds": 2636, + "icu_beds": 140, + "utilization": 0.675049733, + "pct_icu": 5.31 + }, + { + "id": 9, + "name": "Florida", + "abbr": "FL", + "population": 21477737, + "licensed_beds": 61827, + "total_beds": 54821, + "icu_beds": 4979, + "utilization": 0.586008503, + "pct_icu": 9.08 + }, + { + "id": 10, + "name": "Georgia", + "abbr": "GA", + "population": 10617423, + "licensed_beds": 27525, + "total_beds": 23227, + "icu_beds": 2365, + "utilization": 0.545817284, + "pct_icu": 10.18 + }, + { + "id": 11, + "name": "Hawaii", + "abbr": "HI", + "population": 1415872, + "licensed_beds": 3840, + "total_beds": 3361, + "icu_beds": 189, + "utilization": 0.566713418, + "pct_icu": 5.62 + }, + { + "id": 12, + "name": "Iowa", + "abbr": "IA", + "population": 3155070, + "licensed_beds": 11647, + "total_beds": 7749, + "icu_beds": 405, + "utilization": 0.300301859, + "pct_icu": 5.23 + }, + { + "id": 13, + "name": "Idaho", + "abbr": "ID", + "population": 1787147, + "licensed_beds": 3729, + "total_beds": 3325, + "icu_beds": 300, + "utilization": 0.370703648, + "pct_icu": 9.02 + }, + { + "id": 14, + "name": "Illinois", + "abbr": "IL", + "population": 12671821, + "licensed_beds": 36911, + "total_beds": 31103, + "icu_beds": 2589, + "utilization": 0.459973565, + "pct_icu": 8.32 + }, + { + "id": 15, + "name": "Indiana", + "abbr": "IN", + "population": 6732219, + "licensed_beds": 17570, + "total_beds": 17559, + "icu_beds": 1571, + "utilization": 0.469576774, + "pct_icu": 8.95 + }, + { + "id": 16, + "name": "Kansas", + "abbr": "KS", + "population": 2913314, + "licensed_beds": 12507, + "total_beds": 8701, + "icu_beds": 737, + "utilization": 0.379706044, + "pct_icu": 8.47 + }, + { + "id": 17, + "name": "Kentucky", + "abbr": "KY", + "population": 4467673, + "licensed_beds": 16537, + "total_beds": 12975, + "icu_beds": 1303, + "utilization": 0.465596826, + "pct_icu": 10.04 + }, + { + "id": 18, + "name": "Louisiana", + "abbr": "LA", + "population": 4648794, + "licensed_beds": 20245, + "total_beds": 17280, + "icu_beds": 1221, + "utilization": 0.49202741, + "pct_icu": 7.07 + }, + { + "id": 19, + "name": "Massachusetts", + "abbr": "MA", + "population": 6949503, + "licensed_beds": 19240, + "total_beds": 18360, + "icu_beds": 1223, + "utilization": 0.661852196, + "pct_icu": 6.66 + }, + { + "id": 20, + "name": "Maryland", + "abbr": "MD", + "population": 6045680, + "licensed_beds": 12853, + "total_beds": 10873, + "icu_beds": 923, + "utilization": 0.675218296, + "pct_icu": 8.49 + }, + { + "id": 21, + "name": "Maine", + "abbr": "ME", + "population": 1344212, + "licensed_beds": 3887, + "total_beds": 3073, + "icu_beds": 212, + "utilization": 0.528423503, + "pct_icu": 6.9 + }, + { + "id": 22, + "name": "Michigan", + "abbr": "MI", + "population": 9986857, + "licensed_beds": 26132, + "total_beds": 24236, + "icu_beds": 1932, + "utilization": 0.45971872, + "pct_icu": 7.97 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"pct_icu": 7.16 + }, + { + "id": 28, + "name": "North Dakota", + "abbr": "ND", + "population": 762062, + "licensed_beds": 3264, + "total_beds": 3230, + "icu_beds": 208, + "utilization": 0.36541652, + "pct_icu": 6.44 + }, + { + "id": 29, + "name": "Nebraska", + "abbr": "NE", + "population": 1934408, + "licensed_beds": 6436, + "total_beds": 5753, + "icu_beds": 431, + "utilization": 0.293164769, + "pct_icu": 7.49 + }, + { + "id": 30, + "name": "New Hampshire", + "abbr": "NH", + "population": 1359711, + "licensed_beds": 3481, + "total_beds": 2789, + "icu_beds": 240, + "utilization": 0.5802499, + "pct_icu": 8.61 + }, + { + "id": 31, + "name": "New Jersey", + "abbr": "NJ", + "population": 8882190, + "licensed_beds": 26674, + "total_beds": 21365, + "icu_beds": 1437, + "utilization": 0.658698189, + "pct_icu": 6.73 + }, + { + "id": 32, + "name": "New Mexico", + "abbr": "NM", + "population": 2096829, + "licensed_beds": 4867, + "total_beds": 4459, + "icu_beds": 321, + "utilization": 0.423301022, 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--git a/lib/BaltimoreCyberTrustRoot.crt.pem b/lib/BaltimoreCyberTrustRoot.crt.pem new file mode 100644 index 0000000..2bd16eb --- /dev/null +++ b/lib/BaltimoreCyberTrustRoot.crt.pem @@ -0,0 +1,22 @@ +-----BEGIN CERTIFICATE----- +MIIDdzCCAl+gAwIBAgIEAgAAuTANBgkqhkiG9w0BAQUFADBaMQswCQYDVQQGEwJJ +RTESMBAGA1UEChMJQmFsdGltb3JlMRMwEQYDVQQLEwpDeWJlclRydXN0MSIwIAYD +VQQDExlCYWx0aW1vcmUgQ3liZXJUcnVzdCBSb290MB4XDTAwMDUxMjE4NDYwMFoX +DTI1MDUxMjIzNTkwMFowWjELMAkGA1UEBhMCSUUxEjAQBgNVBAoTCUJhbHRpbW9y +ZTETMBEGA1UECxMKQ3liZXJUcnVzdDEiMCAGA1UEAxMZQmFsdGltb3JlIEN5YmVy +VHJ1c3QgUm9vdDCCASIwDQYJKoZIhvcNAQEBBQADggEPADCCAQoCggEBAKMEuyKr +mD1X6CZymrV51Cni4eiVgLGw41uOKymaZN+hXe2wCQVt2yguzmKiYv60iNoS6zjr +IZ3AQSsBUnuId9Mcj8e6uYi1agnnc+gRQKfRzMpijS3ljwumUNKoUMMo6vWrJYeK +mpYcqWe4PwzV9/lSEy/CG9VwcPCPwBLKBsua4dnKM3p31vjsufFoREJIE9LAwqSu +XmD+tqYF/LTdB1kC1FkYmGP1pWPgkAx9XbIGevOF6uvUA65ehD5f/xXtabz5OTZy +dc93Uk3zyZAsuT3lySNTPx8kmCFcB5kpvcY67Oduhjprl3RjM71oGDHweI12v/ye +jl0qhqdNkNwnGjkCAwEAAaNFMEMwHQYDVR0OBBYEFOWdWTCCR1jMrPoIVDaGezq1 +BE3wMBIGA1UdEwEB/wQIMAYBAf8CAQMwDgYDVR0PAQH/BAQDAgEGMA0GCSqGSIb3 +DQEBBQUAA4IBAQCFDF2O5G9RaEIFoN27TyclhAO992T9Ldcw46QQF+vaKSm2eT92 +9hkTI7gQCvlYpNRhcL0EYWoSihfVCr3FvDB81ukMJY2GQE/szKN+OMY3EU/t3Wgx +jkzSswF07r51XgdIGn9w/xZchMB5hbgF/X++ZRGjD8ACtPhSNzkE1akxehi/oCr0 +Epn3o0WC4zxe9Z2etciefC7IpJ5OCBRLbf1wbWsaY71k5h+3zvDyny67G7fyUIhz +ksLi4xaNmjICq44Y3ekQEe5+NauQrz4wlHrQMz2nZQ/1/I6eYs9HRCwBXbsdtTLS +R9I4LtD+gdwyah617jzV/OeBHRnDJELqYzmp +-----END CERTIFICATE----- + diff --git a/lib/arrayMath.ts b/lib/arrayMath.ts new file mode 100644 index 0000000..595fbe7 --- /dev/null +++ b/lib/arrayMath.ts @@ -0,0 +1,26 @@ +export function cumsum(values: Array) { + let sum = 0 + return Array.from(values, v => (sum += v || 0)) +} + +export function maxIndex(values: Array) { + let max = -Infinity + let maxIndex = -1 + let index = -1 + for (const value of values) { + ++index + if (value != null && max < value) { + ;(max = value), (maxIndex = index) + } + } + return maxIndex +} + +export function elementSum(arrays: Array) { + const filtered = arrays.filter(a => a !== null) as number[][] + return filtered.reduce((memo, arr) => arr!.map((el, i) => memo![i] + el, [])) +} + +export function last(array: number[]) { + return array[array.length - 1] +} diff --git a/lib/assertions.ts b/lib/assertions.ts new file mode 100644 index 0000000..0f12d1f --- /dev/null +++ b/lib/assertions.ts @@ -0,0 +1,29 @@ +/** + * Assert that a value is a string and return the string value. + * + * @param v A value to assert is a string + * @param message A message for a thrown error if the value is not a string + */ +export function assertString(v: unknown, message?: string): string { + if (typeof v !== 'string') { + throw new Error(message ?? 'Expected value to be a string') + } + + return v +} + +/** + * Assert that an enviornment variable exists, and fetch it. + * + * @param k The env var key to get + * @param ignoreLocalMode Whether to ignore absence in local mode, and return an empty string if unset + */ +export function assertEnv(k: string, ignoreLocalMode: boolean = false): string { + const value = process.env[k] + + if (value == null && ignoreLocalMode && process.env.LOCAL_MODE) { + return '' + } + + return assertString(value, `Missing env var "${k}"`) +} diff --git a/lib/dateFunctions.ts b/lib/dateFunctions.ts new file mode 100644 index 0000000..3341f88 --- /dev/null +++ b/lib/dateFunctions.ts @@ -0,0 +1,50 @@ +import {DateTime} from 'luxon' +import {ISODate} from '../types/model-runner' + +export function toYYYYMMDD(date?: Date) { + // ensure UTC date is the same as date in current TZ + if (!date || Number.isNaN(date.getTime())) { + date = new Date() + date.setMinutes(date.getMinutes() - date.getTimezoneOffset()) + } + return date.toISOString().substring(0, 10) +} + +export function isValidDate(d: string): boolean { + return !!(d && d.length === 10 && new Date(d).getTime()) +} + +export function addDays(d: ISODate, days: number): ISODate { + return DateTime.fromISO(d) + .plus({days}) + .toISODate() +} + +/** + * Finds the maximum date of an array of ISO dates. + * + * @param dates ISO Date strings to find the max for + */ +export function maxDate(...dates: ISODate[]): ISODate { + return dates.reduce((greatestDate, date) => { + if (!greatestDate) { + return date + } + + if (!date) { + return greatestDate + } + + return greatestDate.localeCompare(date) > 0 ? greatestDate : date + }, '') +} + +/** + * + * @param subject + * @param object + * @return true if subject is greater than object + */ +export function isGreater(thisDate: ISODate, other: ISODate): boolean { + return thisDate.localeCompare(other) > 0 +} diff --git a/lib/db.ts b/lib/db.ts new file mode 100644 index 0000000..c8d95d1 --- /dev/null +++ b/lib/db.ts @@ -0,0 +1,512 @@ +import omit from 'lodash/omit' +import {DateTime} from 'luxon' +import {ServerlessMysql} from 'serverless-mysql' +import SQL from 'sql-template-strings' +import Models from '../lib/models' +import {CaseData} from '../types/case-data' +import {ISODate, ModelInput, RunStatus} from '../types/model-runner' +import {initSentry} from './sentry' +import {Session} from './session' +import { + InterventionData, + InterventionMap, + ParameterAbbreviations +} from './simulation-types' + +const {captureException} = initSentry() + +export type Simulation = { + id: number + region_name: string + status: RunStatus + subregion_name: string | undefined + region_id: string + subregion_id: string | undefined + github_user_id: number + github_user_login: string + configuration: ModelInput + model_runs: ModelRun[] + label: string + created_at: string + updated_at: string +} + +export type ModelRun = { + model_slug: string + status: RunStatus + results_data: string | null + export_location: string | null +} + +export type SimulationSummary = Omit< + Simulation, + 'configuration' | 'model_runs' +> & { + region: string + status: RunStatus + configurationSummary: string +} + +// RowDataPacket is an un-exported type from the Node.js MySQL lib. +type RowDataPacket = {} + +export async function getFatalityData( + conn: ServerlessMysql, + regionID: string, + subregionID: string | undefined, + t0: string, + extent: [number, number] +): Promise { + const t0Date = new Date(t0) + const earliestDate = new Date(t0Date.getTime()) + earliestDate.setDate(t0Date.getDate() + extent[0]) + const latestDate = new Date(t0Date.getTime()) + latestDate.setDate(t0Date.getDate() + extent[1]) + + const query = SQL` + SELECT + date, confirmed, deaths + FROM case_data + WHERE + region_id = ${regionID} AND` + + if (subregionID) { + query.append(SQL`\nsubregion_id = ${subregionID} AND`) + } + + query.append(SQL`\ndate >= ${earliestDate} AND + date <= ${latestDate} + ORDER BY date ASC`) + + const rows = await conn.query< + {date: string; confirmed: number; deaths: number}[] + >(query) + + // Add one to account for t0 itself, I think... + const deaths = new Array(extent[1] - extent[0] + 1).fill(null) + const cumulativeDeaths = new Array(extent[1] - extent[0] + 1).fill(null) + const confirmed = new Array(extent[1] - extent[0] + 1).fill(null) + const cumulativeConfirmed = new Array(extent[1] - extent[0] + 1).fill(null) + + const msPerDay = 1000 * 60 * 60 * 24 + const numRows = rows.length + + for (let i = 0; i < numRows; i++) { + const row = rows[i] + const lastRow = rows[i - 1] + + const date = new Date(row.date) + + const diffFromStart = Math.floor( + (date.getTime() - earliestDate.getTime()) / msPerDay + ) + + deaths[diffFromStart] = row.deaths - (lastRow?.deaths ?? 0) + confirmed[diffFromStart] = row.confirmed - (lastRow?.confirmed ?? 0) + cumulativeDeaths[diffFromStart] = row.deaths + cumulativeConfirmed[diffFromStart] = row.confirmed + } + + return {deaths, cumulativeDeaths, confirmed, cumulativeConfirmed} +} + +export async function getInterventionData( + conn: ServerlessMysql +): Promise { + type Row = { + region_id: string + subregion_id: string + policy: string + notes?: string + source?: string + issue_date: string + start_date?: string + ease_date?: string + expiration_date?: string + end_date?: string + } + + const rows = await conn.query(SQL` + SELECT + region_id, subregion_id, policy, issue_date, + start_date, expiration_date, end_date + FROM + intervention_data; + `) + + const result: any = {} + for (const row of rows) { + const region = row.region_id + const subregion = row.subregion_id || '_self' + const regionData = result[region] || (result[region] = {}) + const subregionData = regionData[subregion] || (regionData[subregion] = {}) + const policyData = (subregionData[row.policy] = {} as InterventionData) + + // To save bytes when serializing, don't add null values. + if (row.issue_date) policyData.dateIssued = row.issue_date + if (row.start_date) policyData.dateEnacted = row.start_date + if (row.expiration_date) policyData.dateExpiry = row.expiration_date + if (row.end_date) policyData.dateEnded = row.end_date + } + + return result +} + +export async function createSimulation( + conn: ServerlessMysql, + props: { + region_id: string + subregion_id?: string + status: RunStatus + github_user_id: string + github_user_login: string + label: string + configuration: Omit + } +): Promise<{insertId: number}> { + return conn.query(SQL` + INSERT INTO simulation_runs ( + github_user_id, + github_user_login, + label, + configuration, + model_runs, + region_id, + subregion_id, + created_at, + updated_at + ) VALUES ( + ${props.github_user_id}, + ${props.github_user_login}, + ${props.label}, + ${JSON.stringify(props.configuration)}, + ${JSON.stringify( + Object.keys(Models).map(slug => ({ + model_slug: slug, + status: props.status, + results_data: null, + export_location: null + })) + )}, + ${props.region_id}, + ${props.subregion_id}, + ${new Date()}, + ${new Date()} + )`) +} + +export async function updateSimulation( + conn: ServerlessMysql, + id: string, + status: RunStatus, + model: string, + resultsLocation: string, + exportLocation: string, + workflowRunID: string | undefined +): Promise { + console.log( + `Updating simulation ${id}/${model} as ${status} at ${resultsLocation}` + ) + + await conn.query('START TRANSACTION') + + const simulationResult = await conn.query< + {id: number; model_runs: ModelRun[]}[] + >( + SQL`SELECT id, model_runs FROM simulation_runs WHERE simulation_runs.id = ${id} FOR UPDATE` + ) + + let affectedRows + + try { + if (simulationResult.length < 1) { + return false + } + + const simulation = simulationResult[0] + + const newModelRuns = simulation.model_runs.map(modelRun => { + if (modelRun.model_slug === model) { + return { + ...modelRun, + results_data: resultsLocation, + export_location: exportLocation, + status + } + } + + return modelRun + }) + + const query = SQL`UPDATE simulation_runs SET model_runs=${JSON.stringify( + newModelRuns + )}` + + if (workflowRunID) { + query.append(SQL`, workflow_run_id=${workflowRunID}`) + } + + query.append(SQL` WHERE id=${id}`) + + const updateResult = await conn.query<{affectedRows: number}>(query) + affectedRows = updateResult.affectedRows + + await conn.query('COMMIT') + } catch (err) { + await conn.query('ROLLBACK') + throw err + } + + return Boolean(affectedRows) +} + +export async function listSimulationSummaries( + conn: ServerlessMysql, + githubUserID: string, + queryOpts?: {region?: string; limit?: number} +): Promise { + const select = SQL`SELECT + simulation_runs.id, + simulation_runs.github_user_id, + simulation_runs.github_user_login, + regions.name AS region_name, + subregions.name AS subregion_name, + regions.id AS region_id, + subregions.id AS subregion_id, + simulation_runs.configuration, + simulation_runs.model_runs, + simulation_runs.label, + DATE_FORMAT(simulation_runs.created_at, "%Y-%m-%dT%TZ") AS created_at, + DATE_FORMAT(simulation_runs.updated_at, "%Y-%m-%dT%TZ") AS updated_at + FROM simulation_runs + INNER JOIN regions AS regions + ON regions.id = simulation_runs.region_id + LEFT JOIN regions AS subregions + ON subregions.id = simulation_runs.subregion_id + WHERE` + + if (queryOpts?.region) { + select.append(SQL` simulation_runs.region_id = ${queryOpts.region} AND`) + } + + select.append( + SQL` simulation_runs.github_user_id = ${githubUserID} ORDER BY updated_at DESC` + ) + + if (queryOpts?.limit != null) { + select.append(SQL` LIMIT ${queryOpts.limit}`) + } + + const results = await conn.query(select) + return (results as Simulation[]).map(summarizeStrategies) +} + +function summarizeStrategies(simulation: Simulation): SimulationSummary { + const summary = omit(simulation, 'configuration') as SimulationSummary + summary.status = getRunStatus(simulation) + + try { + if (!simulation.configuration) { + summary.configurationSummary = '' + } else { + const input = simulation.configuration as ModelInput + summary.configurationSummary = Object.keys(input.parameters) + .map(key => ParameterAbbreviations[key] || '') + .filter(val => val) + .join(' ') + } + } catch (err) { + captureException(err) + console.error(simulation.configuration) + console.error(err) + summary.configurationSummary = 'Invalid parameters' + } + return summary +} + +export async function getRegionCaseData( + conn: ServerlessMysql, + regionID: string, + subregionID: string | undefined +): Promise<{ + deaths: number | null + confirmed: number | null + endDate: ISODate | null +}> { + const subregionQuery = subregionID + ? SQL`\nAND subregion_id = ${subregionID}` + : '\n' + + // We want the death data for the week starting with the most recent data we have + // This isn't the most efficient way of doing it and we could do this all in one + // query. + const endDateQuery = SQL`SELECT + d.date, d.deaths, d.confirmed + FROM case_data AS d + WHERE + d.region_id = ${regionID}` + .append(subregionQuery) + .append(SQL` ORDER BY d.date DESC LIMIT 1`) + const endDateResult = await conn.query< + {date: string; deaths: number; confirmed: number}[] + >(endDateQuery) + + if (!endDateResult.length) { + return { + deaths: null, + confirmed: null, + endDate: null + } + } + return { + deaths: endDateResult[0].deaths, + confirmed: endDateResult[0].confirmed, + endDate: DateTime.fromSQL(endDateResult[0].date).toISODate() + } +} + +export async function getSimulation( + conn: ServerlessMysql, + githubUser: Session['user'], + queryOpts: {id: number} +): Promise { + const isAdmin = await isAdminUser(conn, githubUser.login) + + const query = SQL`SELECT + simulation_runs.id, + simulation_runs.github_user_id, + simulation_runs.github_user_login, + regions.name AS region_name, + subregions.name AS subregion_name, + regions.id AS region_id, + subregions.id AS subregion_id, + simulation_runs.configuration, + simulation_runs.model_runs, + simulation_runs.label, + DATE_FORMAT(simulation_runs.created_at, "%Y-%m-%dT%TZ") AS created_at, + DATE_FORMAT(simulation_runs.updated_at, "%Y-%m-%dT%TZ") AS updated_at + FROM simulation_runs + INNER JOIN regions AS regions + ON regions.id = simulation_runs.region_id + LEFT JOIN regions AS subregions + ON subregions.id = simulation_runs.subregion_id + WHERE + simulation_runs.id = ${queryOpts.id}` + + if (!isAdmin) { + query.append(SQL`\nAND simulation_runs.github_user_id = ${githubUser.id}`) + } + + const results = await conn.query(query) + + if (results.length < 1) { + return null + } + + if (results.length > 1) { + throw new Error(`Multiple simulations found with same id ${queryOpts.id}.`) + } + + return toSimulation(results[0]) +} + +export async function isAuthorizedUser(conn: ServerlessMysql, login: string) { + const results = await conn.query( + SQL`SELECT 1 FROM authorized_users WHERE github_user_login = ${login} LIMIT 1` + ) + + return results.length > 0 +} + +export async function isAdminUser(conn: ServerlessMysql, login: string) { + const results = await conn.query( + SQL`SELECT 1 FROM authorized_users WHERE github_user_login = ${login} AND admin = 1 LIMIT 1` + ) + return results.length > 0 +} + +export type UserConfig = { + hasAcceptedDisclaimer?: boolean +} + +export async function getUserConfig( + conn: ServerlessMysql, + login: string +): Promise { + const results = await conn.query<{config: UserConfig}[]>( + SQL`SELECT config FROM authorized_users WHERE github_user_login = ${login} LIMIT 1` + ) + + if (!results) { + throw new Error('No such user found') + } + + return results[0].config +} + +export async function updateUserConfig( + conn: ServerlessMysql, + login: string, + cb: (conf: UserConfig) => UserConfig +): Promise { + await conn.query('START TRANSACTION') + + let newConfig: UserConfig + + try { + const results = await conn.query<{config: UserConfig}[]>( + SQL`SELECT config FROM authorized_users WHERE github_user_login = ${login} LIMIT 1 FOR UPDATE` + ) + + if (!results) { + throw new Error('No such user found') + } + + const {config} = results[0] + + newConfig = cb(config) + + await conn.query( + SQL`UPDATE authorized_users SET config = ${JSON.stringify( + newConfig + )} WHERE github_user_login = ${login}` + ) + + await conn.query('COMMIT') + } catch (err) { + await conn.query('ROLLBACK') + throw err + } + + return newConfig +} + +function toSimulation(object: any): Simulation { + const simulation = Object.assign({}, object) + simulation.status = getRunStatus(object) + return simulation +} + +function getRunStatus(simulation: Simulation): RunStatus { + const statuses = simulation.model_runs.map(run => run.status) + + // Fail fast—if any are failed, we are failed. + if (statuses.some(status => status === RunStatus.Failed)) + return RunStatus.Failed + + // In progress if any are in progress. + if (statuses.some(status => status === RunStatus.InProgress)) + return RunStatus.InProgress + + // Complete if all are complete. + if (statuses.every(status => status === RunStatus.Complete)) + return RunStatus.Complete + + // Only pending if all are pending. + if (statuses.every(status => status === RunStatus.Pending)) + return RunStatus.Pending + + // Otherwise, we must be in progress (this could happen when one has + // completed, but all others are still pending). + return RunStatus.InProgress +} diff --git a/lib/default-contact-reduction.ts b/lib/default-contact-reduction.ts new file mode 100644 index 0000000..788221c --- /dev/null +++ b/lib/default-contact-reduction.ts @@ -0,0 +1,108 @@ +import {Intensity} from '../types/model-runner' +import {InterventionPeriod, StrategyKey} from './new-simulation-state' + +/** + * This module calculates default contact reduction for a combination of + * intervention strategies, represented as bits. + * + * Not all combinations have a default reduction value—particularly less likely + * ones. + */ + +// Bit values for interventions = +const interventionValues: Record> = { + schoolClosure: { + [Intensity.Mild]: 1, + [Intensity.Moderate]: 2, + [Intensity.Aggressive]: 4 + }, + voluntaryHomeQuarantine: { + [Intensity.Mild]: 8, + [Intensity.Moderate]: 16, + [Intensity.Aggressive]: 32 + }, + caseIsolation: { + [Intensity.Mild]: 64, + [Intensity.Moderate]: 128, + [Intensity.Aggressive]: 256 + }, + socialDistancing: { + [Intensity.Mild]: 512, + [Intensity.Moderate]: 1024, + [Intensity.Aggressive]: 2048 + } +} + +// Map of intervention combinations to default contact reduction +const contactReductionTable = (() => { + const iv = interventionValues + const sc = 'schoolClosure' + const hq = 'voluntaryHomeQuarantine' + const ci = 'caseIsolation' + const sd = 'socialDistancing' + const Mi = Intensity.Mild + const Mo = Intensity.Moderate + const Ag = Intensity.Aggressive + + /** + * Data provided by Neil Ferguson of Imperial College, roughly based on + * https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.0050074 + * + * This is a literal copy of the data from "default-contact-reduction.xlsx" + * in the root of this repository. + */ + + return new Map([ + /* SC */ /* HQ */ /* CI */ /* SD */ + /* ---------|------------|------------|----------*/ + [0 /* */ | 0 /* */ | 0 /* */ | 0 /* */, 0], + [0 /* */ | 0 /* */ | 0 /* */ | iv[sd][Mi], 0.1], + [0 /* */ | 0 /* */ | 0 /* */ | iv[sd][Mo], 0.3], + [0 /* */ | 0 /* */ | 0 /* */ | iv[sd][Ag], 0.65], + [0 /* */ | 0 /* */ | iv[ci][Ag] | 0 /* */, 0.15], + [0 /* */ | 0 /* */ | iv[ci][Ag] | iv[sd][Mi], 0.235], + [0 /* */ | 0 /* */ | iv[ci][Ag] | iv[sd][Mo], 0.405], + [0 /* */ | 0 /* */ | iv[ci][Ag] | iv[sd][Ag], 0.7025], + [0 /* */ | iv[hq][Ag] | iv[ci][Ag] | 0 /* */, 0.25], + [0 /* */ | iv[hq][Ag] | iv[ci][Ag] | iv[sd][Mi], 0.325], + [0 /* */ | iv[hq][Ag] | iv[ci][Ag] | iv[sd][Mo], 0.475], + [0 /* */ | iv[hq][Ag] | iv[ci][Ag] | iv[sd][Ag], 0.7375], + [iv[sc][Ag] | 0 /* */ | 0 /* */ | 0 /* */, 0.175], + [iv[sc][Ag] | 0 /* */ | 0 /* */ | iv[sd][Mi], 0.2575], + [iv[sc][Ag] | 0 /* */ | 0 /* */ | iv[sd][Mo], 0.4225], + [iv[sc][Ag] | 0 /* */ | 0 /* */ | iv[sd][Ag], 0.71125], + [iv[sc][Ag] | 0 /* */ | iv[ci][Ag] | 0 /* */, 0.29875], + [iv[sc][Ag] | 0 /* */ | iv[ci][Ag] | iv[sd][Mi], 0.368875], + [iv[sc][Ag] | 0 /* */ | iv[ci][Ag] | iv[sd][Mo], 0.509125], + [iv[sc][Ag] | 0 /* */ | iv[ci][Ag] | iv[sd][Ag], 0.7545625], + [iv[sc][Ag] | iv[hq][Ag] | iv[ci][Ag] | 0 /* */, 0.38125], + [iv[sc][Ag] | iv[hq][Ag] | iv[ci][Ag] | iv[sd][Mi], 0.443125], + [iv[sc][Ag] | iv[hq][Ag] | iv[ci][Ag] | iv[sd][Mo], 0.566875], + [iv[sc][Ag] | iv[hq][Ag] | iv[ci][Ag] | iv[sd][Ag], 0.7834375] + ]) +})() + +export function getDefaultContactReduction( + per: Pick +): number | null { + const sc = per.schoolClosure + ? interventionValues.schoolClosure[per.schoolClosure] + : 0 + const hq = per.voluntaryHomeQuarantine + ? interventionValues.voluntaryHomeQuarantine[per.voluntaryHomeQuarantine] + : 0 + const ci = per.caseIsolation + ? interventionValues.caseIsolation[per.caseIsolation] + : 0 + const sd = per.socialDistancing + ? interventionValues.socialDistancing[per.socialDistancing] + : 0 + + const reduction = contactReductionTable.get(sc | hq | ci | sd) + + if (reduction != null) { + return Math.round(reduction * 100) + } else { + return null + } +} diff --git a/lib/github.ts b/lib/github.ts new file mode 100644 index 0000000..f5b08b5 --- /dev/null +++ b/lib/github.ts @@ -0,0 +1,92 @@ +import axios, {AxiosInstance} from 'axios' +import {assertEnv} from './assertions' + +type APIAccessToken = {access_token: string} +type APIUser = {id: string; login: string} +type APITeamMembership = { + url: string + role: string + state: 'active' | 'pending' +} + +const CLIENT_OPTS = { + baseURL: 'https://api.github.com', + timeout: 5_000, + headers: { + accept: 'application/json', + 'content-type': 'application/json' + } +} + +const api = axios.create(CLIENT_OPTS) + +/** + * Create a new GitHub API client. + */ +export function createClient(opts: {token: string}): AxiosInstance { + return axios.create({ + ...CLIENT_OPTS, + headers: { + ...CLIENT_OPTS.headers, + authorization: `Bearer ${opts.token}` + } + }) +} + +export function deleteAccessToken(opts: {token: string}): Promise { + return axios.delete(`/applications/${assertEnv('GITHUB_CLIENT_ID')}/token`, { + ...CLIENT_OPTS, + auth: { + username: assertEnv('GITHUB_CLIENT_ID'), + password: assertEnv('GITHUB_CLIENT_SECRET') + }, + data: { + access_token: opts.token + } + }) +} + +/** + * Exchange an OAuth code for an API access token. + */ +export async function exchangeCode( + code: string +): Promise<[AxiosInstance, string]> { + const accessTokenResp = await api.post( + '/login/oauth/access_token', + { + client_id: assertEnv('GITHUB_CLIENT_ID'), + client_secret: assertEnv('GITHUB_CLIENT_SECRET'), + code + }, + {baseURL: 'https://github.com'} + ) + + const token = accessTokenResp.data.access_token + + return [createClient({token}), token] +} + +/** + * Get the authenticated user. + */ +export async function getUser(client: AxiosInstance): Promise { + const resp = await client.get('/user') + return resp.data +} + +/** + * Create a repository dispatch event. + */ +export async function repositoryDispatch( + client: AxiosInstance, + repoOwner: string, + repoName: string, + type: string, + payload: any +): Promise { + await client.post(`/repos/${repoOwner}/${repoName}/dispatches`, { + event_type: type, + client_payload: payload + }) +} diff --git a/lib/handle-error.ts b/lib/handle-error.ts new file mode 100644 index 0000000..5162319 --- /dev/null +++ b/lib/handle-error.ts @@ -0,0 +1,32 @@ +import {GetServerSideProps} from 'next' +import {initSentry} from './sentry' + +const {captureException} = initSentry() + +let didAttachHandlers = false +export function catchUnhandledErrors() { + if (didAttachHandlers) return + didAttachHandlers = true + + process.on('unhandledRejection', err => { + captureException(err as Error) + }) + + process.on('uncaughtException', err => { + captureException(err) + }) +} + +export default function handleError

    ( + cb: GetServerSideProps

    +): GetServerSideProps

    { + return async ctx => { + try { + const result = await cb(ctx) + return result + } catch (err) { + captureException(err) + throw err + } + } +} diff --git a/lib/logging.ts b/lib/logging.ts new file mode 100644 index 0000000..0568ef7 --- /dev/null +++ b/lib/logging.ts @@ -0,0 +1,55 @@ +type Value = Record | undefined | null + +/** + * Log an object, recursively, expanding only the first level by default. + * + * Safari has insane behavior around nesting, so YMMV there (although the + * logged data is correct). + * + * @param title The title of the group + * @param value The object to log + * @param level The current nesting level + */ +export function logValue(title: string, value: Value, level: number = 0) { + if (!value) { + return + } + + group( + title, + () => { + // Log all non-object values. + table( + {[title]: value}, + Object.keys(value).filter(key => typeof value[key] !== 'object') + ) + + Object.entries(value).forEach(([key, value]) => { + if (typeof value !== 'object') return + logValue(key, value, level + 1) + }) + }, + level !== 1 + ) +} + +export function group( + title: string, + cb: () => void, + collapsed: boolean = true +) { + console[collapsed ? 'groupCollapsed' : 'group']( + `%c${title}`, + 'color: blue; font-weight: bold' + ) + cb() + console.groupEnd() +} + +export function table(...args: any[]) { + if (typeof console.table === 'function') { + console.table(...args) + } else { + console.log(...args) + } +} diff --git a/lib/models.ts b/lib/models.ts new file mode 100644 index 0000000..84ef362 --- /dev/null +++ b/lib/models.ts @@ -0,0 +1,54 @@ +const isProduction = process.env.APP_ENVIRONMENT === 'production' + +const models: ModelMap = require('../models.yml') + +Object.keys(models).forEach(modelId => { + if (isProduction && !models[modelId].isProductionReady) { + delete models[modelId] + } +}) + +export default models + +export type ModelSpec = { + name: string + origin: string + imageURL: string + metaURLs?: { + code?: string + paper?: string + website?: string + } + description: string + supportedParameters: SupportedParameter[] + isProductionReady: boolean +} + +export type MinimalModelSpec = { + metaURLs?: { + code?: string + paper?: string + website?: string + } +} + +export type ModelMap = {[key: string]: ModelSpec} + +export enum SupportedParameter { + ContactReduction = 'contactReduction', + InterventionStrategies = 'interventionStrategies', + R0 = 'r0' +} + +export function supportedParameterDesc(supportedParameter: SupportedParameter) { + switch (supportedParameter) { + case SupportedParameter.ContactReduction: + return 'Contact reduction is used by' + case SupportedParameter.InterventionStrategies: + return 'Intervention strategies are used by' + case SupportedParameter.R0: + return 'Customizable R0 is used by' + default: + throw new Error('Missing case') + } +} diff --git a/lib/mysql.ts b/lib/mysql.ts new file mode 100644 index 0000000..258e74c --- /dev/null +++ b/lib/mysql.ts @@ -0,0 +1,70 @@ +import {captureException, captureMessage, Severity} from '@sentry/node' +import fs from 'fs' +import {ConnectionConfig} from 'mysql' +import mysql, {ServerlessMysql} from 'serverless-mysql' + +// eslint-disable-next-line @typescript-eslint/ban-ts-ignore +// @ts-ignore: Ensure we aren't using WebPack's version of "path". +const path = __non_webpack_require__('path') + +// Cert URL: https://www.digicert.com/CACerts/BaltimoreCyberTrustRoot.crt.pem + +const host = process.env.DB_HOST +const user = process.env.DB_USERNAME +const password = process.env.DB_PASSWORD +const database = process.env.DB_DATABASE +const config: ConnectionConfig = { + host, + user, + password, + database, + dateStrings: true, + typeCast: (field, next) => { + switch (field.type) { + case 'JSON': + return JSON.parse(field.string()) + default: + return next() + } + } +} + +if (process.env.NODE_ENV === 'production') { + config.ssl = { + ca: fs + .readFileSync( + path.join(process.cwd(), 'lib/BaltimoreCyberTrustRoot.crt.pem') + ) + .toString() + } +} + +const db = mysql({ + config, + maxRetries: 5, + onConnectError: (err: Error) => captureException(err), + onError: (err: Error) => captureException(err), + onKillError: (err: Error) => captureException(err) +}) + +type Callback

    , R> = (...args: P) => Promise + +export const withDB =

    , R>( + cb: (conn: ServerlessMysql) => Callback +): Callback => { + return async (...args: P) => { + try { + const result = await cb(db)(...args) + return result + } finally { + try { + await db.end() + } catch (err) { + captureMessage( + `Error closing DB connection ${err.message}`, + Severity.Warning + ) + } + } + } +} diff --git a/lib/new-simulation-state.ts b/lib/new-simulation-state.ts new file mode 100644 index 0000000..cafd08b --- /dev/null +++ b/lib/new-simulation-state.ts @@ -0,0 +1,405 @@ +import Joi from '@hapi/joi' +import Debug from 'debug' +import omit from 'lodash/omit' +import { + Intensity, + InterventionPeriod as RunnerInterventionPeriod +} from '../types/model-runner' +import {Region, TopLevelRegion} from '../types/regions' +import {addDays, maxDate, toYYYYMMDD} from './dateFunctions' +import {getDefaultContactReduction} from './default-contact-reduction' +import {newSimulationSchema} from './simulation-schema' +import {InterventionMap} from './simulation-types' + +export {Intensity} from '../types/model-runner' + +const debug = Debug('app:new-simulation-state') + +// To be moved to shared location +type ISODate = string + +/** + * The state object used in the react page + */ +export interface NewSimulationState { + region: TopLevelRegion + subregion: Region + label: string + r0: number | undefined + interventionPeriods: InterventionPeriod[] +} + +/** + * The data sent from web UI to backend + */ +export interface NewSimulationConfig { + regionID: string + subregionID?: string + label: string + r0: number | undefined + interventionPeriods: RunnerInterventionPeriod[] +} + +export interface StrategyDescription { + label: string + intensities?: Record +} + +export const StrategyDescriptions: Record = { + socialDistancing: { + label: 'Social Distancing', + intensities: { + [Intensity.Aggressive]: + 'Statewide lockdown (Assumes 90% social contact reduction)', + [Intensity.Moderate]: + 'Stay at Home or state curfew (Assumes 75% social contact reduction)', + [Intensity.Mild]: + 'Restrict any mass gatherings (Assumes 50% social contact reduction)' + } + }, + schoolClosure: {label: 'School Closure'}, + caseIsolation: {label: 'Case Isolation'}, + voluntaryHomeQuarantine: {label: 'Voluntary Home Quarantine'} +} + +export type StrategyKey = + | 'socialDistancing' + | 'schoolClosure' + | 'caseIsolation' + | 'voluntaryHomeQuarantine' + +export interface InterventionPeriod + extends Omit { + isAutoGenerated: boolean + // We need to support an empty string for reductionPopulationContact because + // that is the default value for new periods + reductionPopulationContact: number | '' +} + +/** + * + * @param state simulation state from React UI + * + * @return simulation config required by the back end. + */ +export function createFormBody(state: NewSimulationState): NewSimulationConfig { + return { + regionID: state.region.id, + subregionID: + state.subregion.id !== '_self' ? state.subregion.id : undefined, + label: state.label, + r0: state.r0, + interventionPeriods: state.interventionPeriods.map(period => ({ + ...omit(period, 'isAutoGenerated'), + + // note: allow for invalid values since we check for it later + reductionPopulationContact: + typeof period.reductionPopulationContact === 'number' + ? period.reductionPopulationContact + : ((undefined as unknown) as number) + })) + } +} + +type Action = + | { + type: 'SET_LABEL' + label: string + } + | { + type: 'SET_R0' + r0: number | undefined + } + | { + type: 'SET_REGION' + region: TopLevelRegion + interventions: InterventionMap + } + | { + type: 'SET_SUBREGION' + subregion: Region + interventions: InterventionMap + } + | { + type: 'UPDATE_PERIOD' + period: InterventionPeriod + newPeriod: Partial + } + | { + type: 'UPDATE_PERIOD_INTERVENTIONS' + period: InterventionPeriod + update: Pick + } + | { + type: 'ADD_PERIOD' + period: InterventionPeriod + } + | { + type: 'REMOVE_PERIOD' + period: InterventionPeriod + } + +export function initializeSimulationState( + initialState: Pick, + interventions: InterventionMap +): NewSimulationState { + return { + ...initialState, + r0: undefined, + label: `Simulation created on ${toYYYYMMDD()}`, + interventionPeriods: autoFillParameters( + initialState.region, + initialState.subregion, + interventions + ) + } +} + +export function reducer( + state: NewSimulationState, + action: Action +): NewSimulationState { + debug('reducer state=%O action=%o', state, action) + + switch (action.type) { + case 'SET_LABEL': + return {...state, label: action.label} + + case 'SET_R0': + return {...state, r0: action.r0} + + case 'SET_REGION': + return { + ...state, + region: action.region, + subregion: Object.values(action.region.regions)[0], + interventionPeriods: autoFillParameters( + action.region, + Object.values(action.region.regions)[0], + action.interventions + ) + } + + case 'SET_SUBREGION': + return { + ...state, + subregion: action.subregion, + interventionPeriods: autoFillParameters( + state.region, + action.subregion, + action.interventions + ) + } + + case 'ADD_PERIOD': { + const newPeriod: InterventionPeriod = { + ...action.period, + reductionPopulationContact: + getDefaultContactReduction(action.period) ?? '' + } + const periods = [...state.interventionPeriods, newPeriod] + return { + ...state, + interventionPeriods: periods + } + } + case 'REMOVE_PERIOD': { + const periods = state.interventionPeriods.filter( + period => period !== action.period + ) + return { + ...state, + interventionPeriods: periods + } + } + case 'UPDATE_PERIOD': { + const periods = [...state.interventionPeriods] + const index = periods.findIndex(period => period === action.period) + const newPeriod = { + ...action.period, + ...action.newPeriod, + isAutoGenerated: false + } + periods[index] = newPeriod + return { + ...state, + interventionPeriods: periods + } + } + case 'UPDATE_PERIOD_INTERVENTIONS': { + const periods = [...state.interventionPeriods] + const index = periods.findIndex(period => period === action.period) + const newPeriod = { + ...action.period, + ...action.update, + isAutoGenerated: false + } + + const newReduction = getDefaultContactReduction(newPeriod) + newPeriod.reductionPopulationContact = newReduction ?? '' + + periods[index] = {...newPeriod} + return { + ...state, + interventionPeriods: periods + } + } + } +} + +function autoFillParameters( + region: Region, + subregion: Region | undefined, + interventions: InterventionMap +): InterventionPeriod[] { + if (!subregion || region.id !== 'US') { + return [] + } + const regionInterventions = interventions[region.id][subregion.id] + if (!regionInterventions) { + return [] + } + + const rawInterventions = [] as { + type: StrategyKey + startDate: ISODate + intensity: Intensity + }[] + + function addIntervention( + name: string, + type: StrategyKey, + intensity: Intensity + ) { + const namedInterventions = regionInterventions[name] + if (namedInterventions?.dateEnacted) { + rawInterventions.push({ + type, + intensity, + startDate: namedInterventions.dateEnacted + }) + } + } + addIntervention('SchoolClose', 'schoolClosure', Intensity.Aggressive) + addIntervention('GathRestrict10', 'socialDistancing', Intensity.Mild) + addIntervention('StayAtHome', 'socialDistancing', Intensity.Moderate) + addIntervention('StateCurfew', 'socialDistancing', Intensity.Moderate) + + // Sort by start date and create initial interventions set + let interventionPeriods: InterventionPeriod[] = rawInterventions + .sort((i1, i2) => i1.startDate.localeCompare(i2.startDate)) + .map(raw => ({ + startDate: raw.startDate, + reductionPopulationContact: '', + isAutoGenerated: true, + voluntaryHomeQuarantine: Intensity.Aggressive, + caseIsolation: Intensity.Aggressive, + [raw.type]: raw.intensity + })) + + // merge with previous item and dedup + interventionPeriods = interventionPeriods + .reduce((combined, interventionPeriod, i) => { + combined.push({ + ...(combined[i - 1] || {}), + ...interventionPeriod + }) + return combined + }, [] as InterventionPeriod[]) + .filter((current, i, array) => { + // Remove a period if the next one shares a start date + // This happens when multiple interventions are announced on + // the same day. + const next = array[i + 1] + return !next || next.startDate !== current.startDate + }) + + .filter((current, i, array) => { + // Only show the current period if it is different from previous one + // This happens when interventions change, but not in a way that is + // relevant to our heuristics. + const previous = array[i - 1] + return ( + !previous || + previous.socialDistancing !== current.socialDistancing || + previous.schoolClosure !== current.schoolClosure + ) + }) + + // Apply default reduction in contact. + interventionPeriods = interventionPeriods.map(period => { + const reductionPopulationContact = getDefaultContactReduction(period) + + if (reductionPopulationContact != null) { + return {...period, reductionPopulationContact} + } else { + return period + } + }) + + return interventionPeriods +} + +export function validateSchema( + config: NewSimulationConfig +): Joi.ValidationError | undefined { + const {error} = newSimulationSchema.validate(config, { + abortEarly: false, + // eslint-disable-next-line + // @ts-ignore + errors: {wrap: {label: ''}}, // (Joi TS types are wrong) + messages: { + 'interventions.strategyRequired': + 'Interventions must contain at least one active strategy across all periods', + 'interventions.chronology': + "Start date must be after the previous period's start date", + 'reductionPopulationContact.bounds': + 'Estimated population contact reduction must be between 0% and 100%' + } + }) + + return error +} + +/** + * Finds the start date of the next intervention period to add. + * + * The heuristic is that we choose the current date if the last intervention + * period is before the current date. Otherwise, we use the day after the + * last intervention date. + * + * @param interventionPeriods Current list of interventions + */ +export function getNextInterventionPeriodStart( + interventionPeriods: InterventionPeriod[] +): ISODate { + const today = toYYYYMMDD() + if (!interventionPeriods.length) { + return today + } + const dayAfterLastStartDate = addDays( + interventionPeriods[interventionPeriods.length - 1].startDate, + 1 + ) + return maxDate(today, dayAfterLastStartDate) +} + +/** + * Finds a heuristically reasonable end to all interventions. The heuristic is to + * take 90 days after the start date of the last intervention or today (whichever is greater). + * + * @param interventionPeriods Current list of interventions + */ +export function getInterventionsEnd( + interventionPeriods: InterventionPeriod[] +): ISODate { + const threeMonthsLater = addDays(toYYYYMMDD(), 90) + if (!interventionPeriods.length) { + return threeMonthsLater + } + const threeMonthsAfterLastStartDate = addDays( + interventionPeriods[interventionPeriods.length - 1].startDate, + 90 + ) + return maxDate(threeMonthsLater, threeMonthsAfterLastStartDate) +} diff --git a/lib/redirect.ts b/lib/redirect.ts new file mode 100644 index 0000000..dd23193 --- /dev/null +++ b/lib/redirect.ts @@ -0,0 +1,18 @@ +import {ServerResponse} from 'http' + +/** + * Redirect the response to another location. + * + * @param res The response to redirect + * @param location The path to redirect to + * @param statusCode The HTTP status code + */ +export default function redirect( + res: ServerResponse, + location: string, + statusCode: number = 302 +) { + res.setHeader('location', location) + res.statusCode = statusCode + res.end('found') +} diff --git a/lib/regionEmoji.ts b/lib/regionEmoji.ts new file mode 100644 index 0000000..495554c --- /dev/null +++ b/lib/regionEmoji.ts @@ -0,0 +1,9 @@ +import emojiFlags from 'emoji-flags' + +export default function flagAndName( + regionID: string, + regionName: string +): string { + const country = emojiFlags.countryCode(regionID) + return country ? `${country.emoji} ${regionName}` : regionName +} diff --git a/lib/sentry.ts b/lib/sentry.ts new file mode 100644 index 0000000..14221b0 --- /dev/null +++ b/lib/sentry.ts @@ -0,0 +1,97 @@ +import * as Sentry from '@sentry/node' +import {NextPageContext} from 'next' + +export const initSentry = (release = process.env.SENTRY_RELEASE) => { + const sentryOptions: Sentry.NodeOptions = { + dsn: process.env.SENTRY_DSN, + environment: process.env.APP_ENVIRONMENT, + release, + maxBreadcrumbs: 50, + attachStacktrace: true + } + + if (process.env.NODE_ENV !== 'production') { + sentryOptions.beforeSend = () => null + } + + Sentry.init(sentryOptions) + + return { + Sentry, + + captureMessage: ( + message: string, + level?: Sentry.Severity, + extra?: Record + ) => { + Sentry.configureScope(scope => { + if (process.browser) { + scope.setTag('ssr', 'false') + } else { + scope.setTag('ssr', 'true') + } + + if (extra) for (const k in extra) scope.setExtra(k, extra[k]) + }) + + return Sentry.captureMessage(message, level) + }, + + captureException: (err: Error, errorInfo?: Record) => { + console.error(err) + + Sentry.configureScope(scope => { + if (process.browser) { + scope.setTag('ssr', 'false') + } else { + scope.setTag('ssr', 'true') + } + + if (errorInfo) { + for (const key in errorInfo) { + scope.setExtra(key, errorInfo[key]) + } + } + }) + + return Sentry.captureException(err) + }, + + captureContextException: ( + err: NonNullable, + ctx: NextPageContext + ) => { + console.error(err) + + Sentry.configureScope(scope => { + if (err.message) { + scope.setFingerprint([err.message]) + } + + if (err.statusCode) { + scope.setExtra('statusCode', err.statusCode) + } + + if (ctx) { + const {req, res, query, pathname} = ctx + + if (res?.statusCode) { + scope.setExtra('statusCode', res.statusCode) + } + + if (process.browser) { + scope.setTag('ssr', 'false') + scope.setExtra('query', query) + scope.setExtra('pathname', pathname) + } else { + scope.setTag('ssr', 'true') + scope.setExtra('url', req?.url) + scope.setExtra('method', req?.method) + } + } + }) + + return Sentry.captureException(err) + } + } +} diff --git a/lib/session.ts b/lib/session.ts new file mode 100644 index 0000000..eba7765 --- /dev/null +++ b/lib/session.ts @@ -0,0 +1,125 @@ +import Cookies from 'cookies' +import {IncomingMessage, ServerResponse} from 'http' +import {GetServerSideProps} from 'next' +import {assertEnv} from './assertions' +import redirect from './redirect' + +const isProd = process.env.NODE_ENV === 'production' + +const SET_OPTS: Cookies.SetOption = { + maxAge: 60 * 60 * 24 * 7 * 1000, // 1 week + path: '/', + httpOnly: true, + sameSite: 'lax', + secure: isProd, + signed: isProd +} + +const GET_OPTS: Cookies.GetOption = { + signed: isProd +} + +const SESSION_SECRET = assertEnv('SESSION_SECRET') + +export type Session = {user: {id: string; login: string}} + +/** + * Get the session cookie value from the given request. + * + * @param req The session request + */ +export function getSessionCookie( + req: IncomingMessage, + res: ServerResponse +): Session | null { + const sessionValue = getCookieJar(req, res).get('session', GET_OPTS) + + if (!sessionValue) { + return null + } + + try { + const session = JSON.parse(sessionValue) + return session + } catch (err) { + console.error('Error parsing session cookie') + return null + } +} + +/** + * Set a session on the given response. + * + * @param res The response to set the cookie on + * @param value The value of the session + */ +export function setSessionCookie( + req: IncomingMessage, + res: ServerResponse, + value: Session +) { + getCookieJar(req, res).set('session', JSON.stringify(value), SET_OPTS) +} + +/** + * Clear the session from the response. + * + * @param res The response to clear the session from + */ +export function clearSessionCookie(req: IncomingMessage, res: ServerResponse) { + getCookieJar(req, res).set('session', '', {...SET_OPTS, maxAge: 1}) +} + +function getCookieJar(req: IncomingMessage, res: ServerResponse): Cookies { + return new Cookies(req, res, { + secure: isProd, + keys: [SESSION_SECRET] + }) +} + +/** + * Ensure a session is present before calling the given callback. + */ +export function ensureSession

    ( + cb?: ( + ctx: Parameters>[0], + session: Session + ) => ReturnType> +): GetServerSideProps

    { + return async ctx => { + const session = getSessionCookie(ctx.req, ctx.res) + + if (!session) { + redirect(ctx.res, '/') + return {props: {} as any} + } + + if (cb) { + return cb(ctx, session) + } else { + return {props: {}} + } + } +} + +/** + * Ensure a session is not present before calling the given callback. + */ +export function refuteSession

    ( + cb?: GetServerSideProps

    +): GetServerSideProps

    { + return async ctx => { + const session = getSessionCookie(ctx.req, ctx.res) + + if (session) { + redirect(ctx.res, '/simulations') + return {props: {} as any} + } + + if (cb) { + return cb(ctx) + } else { + return {props: {}} + } + } +} diff --git a/lib/simulation-schema.ts b/lib/simulation-schema.ts new file mode 100644 index 0000000..dda0d4f --- /dev/null +++ b/lib/simulation-schema.ts @@ -0,0 +1,105 @@ +import Joi from '@hapi/joi' +import {Intensity, InterventionPeriod, ISODate} from '../types/model-runner' +import {isGreater} from './dateFunctions' + +export const interventionStrategySchema = Joi.object({ + startDate: Joi.string() + .label('Start date') + .required() + .isoDate() + .custom(validatePeriodsChronology), + reductionPopulationContact: Joi.number() + .label('Estimated population contact reduction') + .required() + .integer() + .custom(validateReductionPerc), + socialDistancing: Joi.string() + .label('Social distancing') + .valid(...Object.values(Intensity)), + schoolClosure: Joi.string() + .label('School closure') + .valid(Intensity.Aggressive), + caseIsolation: Joi.string() + .label('Case isolation') + .valid(Intensity.Aggressive), + voluntaryHomeQuarantine: Joi.string() + .label('Voluntary home quarantine') + .valid(Intensity.Aggressive) +}) + +export const newSimulationSchema = Joi.object({ + regionID: Joi.string() + .label('Region') + .required() + .min(2) + .max(64), + subregionID: Joi.string() + .label('Subregion') + .min(2) + .max(64), + label: Joi.string() + .label('Name') + .max(64) + .allow(''), + interventionPeriods: Joi.array() + .label('Intervention periods') + .required() + .max(32) + .items(interventionStrategySchema) + .custom(validateMinimumOneInterventionStrategy), + r0: Joi.number() + .label('Estimated r0') + .greater(0) +}) + +function validateReductionPerc( + perc: number, + helpers: Joi.CustomHelpers +) { + if (perc < 0 || perc > 100) { + return helpers.error('reductionPopulationContact.bounds') + } + + return perc +} + +function validatePeriodsChronology( + startDate: ISODate, + helpers: Joi.CustomHelpers +) { + // This is a little bit of a cheat because Joi doesn't tell us what index + // we're at in the list. + const path = helpers.state?.path ?? [] + const list = helpers.state.ancestors[1] + const selfIndex = (path[1] as unknown) as number + + if (selfIndex > 0 && !isGreater(startDate, list[selfIndex - 1].startDate)) { + return helpers.error('interventions.chronology') + } + + return startDate +} + +function validateMinimumOneInterventionStrategy( + interventionPeriods: InterventionPeriod[], + helpers: Joi.CustomHelpers +) { + let hasAtLeastOneStrategy = false + + for (const period of interventionPeriods) { + let hasStrategy = false + if (period.socialDistancing != null) hasStrategy = true + if (period.schoolClosure != null) hasStrategy = true + if (period.caseIsolation != null) hasStrategy = true + if (period.voluntaryHomeQuarantine != null) hasStrategy = true + + if (hasStrategy) { + hasAtLeastOneStrategy = true + break + } + } + + if (!hasAtLeastOneStrategy) { + return helpers.error('interventions.strategyRequired') + } +} diff --git a/lib/simulation-types.ts b/lib/simulation-types.ts new file mode 100644 index 0000000..7056c0e --- /dev/null +++ b/lib/simulation-types.ts @@ -0,0 +1,69 @@ +export enum Virus { + Covid19 = 'covid19' +} + +export enum SimulationStatus { + Complete = 'complete', + InProgress = 'in-progress', + Failed = 'failed', + Pending = 'pending' +} + +export interface ErrorSimulationData { + error: string + status: SimulationStatus.Failed +} + +export function virusName(virus: Virus): string { + switch (virus) { + case Virus.Covid19: + return 'COVID-19' + } +} + +type ISODate = string + +export const ParameterAbbreviations: Record = { + caseIsolation: 'CI', + schoolClosure: 'SC', + socialDistancing: 'SD', + voluntaryHomeQuarantine: 'VHQ' +} + +export const InterventionNames = { + schoolClosure: 'School Closures', + socialDistancing: 'Social Distancing (Everyone)', + caseIsolation: 'Case Isolation', + voluntaryHomeQuarantine: 'Voluntary Home Quarantine' +} + +export type InterventionName = keyof typeof InterventionNames + +/** + * This is one intervention entry for one state in our interventions data + */ +export interface InterventionData { + dateIssued: ISODate + dateEnacted: ISODate + dateExpiry: ISODate + dateEnded: ISODate + notes: string + source: string +} + +/** + * This is intervention data for an entire state + */ +export interface Interventions { + // The two interventions that we use right now are SchoolClose and StayAtHome + SchoolClose?: InterventionData + StayAtHome?: InterventionData + [key: string]: InterventionData | undefined +} + +/** + * This is all of our interventions data + */ +export interface InterventionMap { + US: Record +} diff --git a/migrations/.gitkeep b/migrations/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/migrations/20200331170118-create-simulations-runs-table.js b/migrations/20200331170118-create-simulations-runs-table.js new file mode 100644 index 0000000..3daae18 --- /dev/null +++ b/migrations/20200331170118-create-simulations-runs-table.js @@ -0,0 +1,59 @@ +'use strict' + +var dbm +var type +var seed +var fs = require('fs') +var path = require('path') +var Promise + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate + type = dbm.dataType + seed = seedLink + Promise = options.Promise +} + +exports.up = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200331170118-create-simulations-runs-table-up.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports.down = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200331170118-create-simulations-runs-table-down.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports._meta = { + version: 1 +} diff --git a/migrations/20200331210801-create-locations-table.js b/migrations/20200331210801-create-locations-table.js new file mode 100644 index 0000000..e6cced0 --- /dev/null +++ b/migrations/20200331210801-create-locations-table.js @@ -0,0 +1,53 @@ +'use strict'; + +var dbm; +var type; +var seed; +var fs = require('fs'); +var path = require('path'); +var Promise; + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate; + type = dbm.dataType; + seed = seedLink; + Promise = options.Promise; +}; + +exports.up = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200331210801-create-locations-table-up.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports.down = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200331210801-create-locations-table-down.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports._meta = { + "version": 1 +}; diff --git a/migrations/20200331233621-add-github-user-login-to-simulation-runs.js b/migrations/20200331233621-add-github-user-login-to-simulation-runs.js new file mode 100644 index 0000000..f59b285 --- /dev/null +++ b/migrations/20200331233621-add-github-user-login-to-simulation-runs.js @@ -0,0 +1,59 @@ +'use strict' + +var dbm +var type +var seed +var fs = require('fs') +var path = require('path') +var Promise + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate + type = dbm.dataType + seed = seedLink + Promise = options.Promise +} + +exports.up = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200331233621-add-github-user-login-to-simulation-runs-up.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports.down = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200331233621-add-github-user-login-to-simulation-runs-down.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports._meta = { + version: 1 +} diff --git a/migrations/20200402165609-drop-location-id-from-simulation-runs.js b/migrations/20200402165609-drop-location-id-from-simulation-runs.js new file mode 100644 index 0000000..a5ba610 --- /dev/null +++ b/migrations/20200402165609-drop-location-id-from-simulation-runs.js @@ -0,0 +1,59 @@ +'use strict' + +var dbm +var type +var seed +var fs = require('fs') +var path = require('path') +var Promise + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate + type = dbm.dataType + seed = seedLink + Promise = options.Promise +} + +exports.up = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200402165609-drop-location-id-from-simulation-runs-up.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports.down = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200402165609-drop-location-id-from-simulation-runs-down.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports._meta = { + version: 1 +} diff --git a/migrations/20200402165728-create-regions-table.js b/migrations/20200402165728-create-regions-table.js new file mode 100644 index 0000000..2128eb6 --- /dev/null +++ b/migrations/20200402165728-create-regions-table.js @@ -0,0 +1,59 @@ +'use strict' + +var dbm +var type +var seed +var fs = require('fs') +var path = require('path') +var Promise + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate + type = dbm.dataType + seed = seedLink + Promise = options.Promise +} + +exports.up = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200402165728-create-regions-table-up.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports.down = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200402165728-create-regions-table-down.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports._meta = { + version: 1 +} diff --git a/migrations/20200402165838-add-iso-region-columns-to-simulation-runs.js b/migrations/20200402165838-add-iso-region-columns-to-simulation-runs.js new file mode 100644 index 0000000..4705bc2 --- /dev/null +++ b/migrations/20200402165838-add-iso-region-columns-to-simulation-runs.js @@ -0,0 +1,59 @@ +'use strict' + +var dbm +var type +var seed +var fs = require('fs') +var path = require('path') +var Promise + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate + type = dbm.dataType + seed = seedLink + Promise = options.Promise +} + +exports.up = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200402165838-add-iso-region-columns-to-simulation-runs-up.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports.down = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200402165838-add-iso-region-columns-to-simulation-runs-down.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports._meta = { + version: 1 +} diff --git a/migrations/20200402172411-drop-locations-table.js b/migrations/20200402172411-drop-locations-table.js new file mode 100644 index 0000000..a7917c1 --- /dev/null +++ b/migrations/20200402172411-drop-locations-table.js @@ -0,0 +1,59 @@ +'use strict' + +var dbm +var type +var seed +var fs = require('fs') +var path = require('path') +var Promise + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate + type = dbm.dataType + seed = seedLink + Promise = options.Promise +} + +exports.up = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200402172411-drop-locations-table-up.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports.down = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200402172411-drop-locations-table-down.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports._meta = { + version: 1 +} diff --git a/migrations/20200402181839-insert-default-region.js b/migrations/20200402181839-insert-default-region.js new file mode 100644 index 0000000..0b43248 --- /dev/null +++ b/migrations/20200402181839-insert-default-region.js @@ -0,0 +1,59 @@ +'use strict' + +var dbm +var type +var seed +var fs = require('fs') +var path = require('path') +var Promise + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate + type = dbm.dataType + seed = seedLink + Promise = options.Promise +} + +exports.up = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200402181839-insert-default-region-up.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports.down = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200402181839-insert-default-region-down.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports._meta = { + version: 1 +} diff --git a/migrations/20200404153055-add-workflow-run-id-to-simulation-runs.js b/migrations/20200404153055-add-workflow-run-id-to-simulation-runs.js new file mode 100644 index 0000000..18a28e6 --- /dev/null +++ b/migrations/20200404153055-add-workflow-run-id-to-simulation-runs.js @@ -0,0 +1,53 @@ +'use strict'; + +var dbm; +var type; +var seed; +var fs = require('fs'); +var path = require('path'); +var Promise; + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate; + type = dbm.dataType; + seed = seedLink; + Promise = options.Promise; +}; + +exports.up = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200404153055-add-workflow-run-id-to-simulation-runs-up.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports.down = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200404153055-add-workflow-run-id-to-simulation-runs-down.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports._meta = { + "version": 1 +}; diff --git a/migrations/20200406164833-add-github-user-id-index-to-simulation-runs.js b/migrations/20200406164833-add-github-user-id-index-to-simulation-runs.js new file mode 100644 index 0000000..7d5d369 --- /dev/null +++ b/migrations/20200406164833-add-github-user-id-index-to-simulation-runs.js @@ -0,0 +1,53 @@ +'use strict'; + +var dbm; +var type; +var seed; +var fs = require('fs'); +var path = require('path'); +var Promise; + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate; + type = dbm.dataType; + seed = seedLink; + Promise = options.Promise; +}; + +exports.up = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200406164833-add-github-user-id-index-to-simulation-runs-up.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports.down = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200406164833-add-github-user-id-index-to-simulation-runs-down.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports._meta = { + "version": 1 +}; diff --git a/migrations/20200406180709-rename-uk-to-gb.js b/migrations/20200406180709-rename-uk-to-gb.js new file mode 100644 index 0000000..f5c4571 --- /dev/null +++ b/migrations/20200406180709-rename-uk-to-gb.js @@ -0,0 +1,53 @@ +'use strict'; + +var dbm; +var type; +var seed; +var fs = require('fs'); +var path = require('path'); +var Promise; + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate; + type = dbm.dataType; + seed = seedLink; + Promise = options.Promise; +}; + +exports.up = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200406180709-rename-uk-to-gb-up.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports.down = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200406180709-rename-uk-to-gb-down.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports._meta = { + "version": 1 +}; diff --git a/migrations/20200406183238-create-authorized-users.js b/migrations/20200406183238-create-authorized-users.js new file mode 100644 index 0000000..a01e607 --- /dev/null +++ b/migrations/20200406183238-create-authorized-users.js @@ -0,0 +1,53 @@ +'use strict'; + +var dbm; +var type; +var seed; +var fs = require('fs'); +var path = require('path'); +var Promise; + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate; + type = dbm.dataType; + seed = seedLink; + Promise = options.Promise; +}; + +exports.up = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200406183238-create-authorized-users-up.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports.down = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200406183238-create-authorized-users-down.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports._meta = { + "version": 1 +}; diff --git a/migrations/20200406191215-insert-us-subregions.js b/migrations/20200406191215-insert-us-subregions.js new file mode 100644 index 0000000..0a3f679 --- /dev/null +++ b/migrations/20200406191215-insert-us-subregions.js @@ -0,0 +1,53 @@ +'use strict'; + +var dbm; +var type; +var seed; +var fs = require('fs'); +var path = require('path'); +var Promise; + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate; + type = dbm.dataType; + seed = seedLink; + Promise = options.Promise; +}; + +exports.up = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200406191215-insert-us-subregions-up.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports.down = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200406191215-insert-us-subregions-down.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports._meta = { + "version": 1 +}; diff --git a/migrations/20200406222239-insert-ak-hi.js b/migrations/20200406222239-insert-ak-hi.js new file mode 100644 index 0000000..f845265 --- /dev/null +++ b/migrations/20200406222239-insert-ak-hi.js @@ -0,0 +1,53 @@ +'use strict'; + +var dbm; +var type; +var seed; +var fs = require('fs'); +var path = require('path'); +var Promise; + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate; + type = dbm.dataType; + seed = seedLink; + Promise = options.Promise; +}; + +exports.up = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200406222239-insert-ak-hi-up.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports.down = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200406222239-insert-ak-hi-down.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports._meta = { + "version": 1 +}; diff --git a/migrations/20200407175551-create-case-data-table.js b/migrations/20200407175551-create-case-data-table.js new file mode 100644 index 0000000..dca3437 --- /dev/null +++ b/migrations/20200407175551-create-case-data-table.js @@ -0,0 +1,53 @@ +'use strict'; + +var dbm; +var type; +var seed; +var fs = require('fs'); +var path = require('path'); +var Promise; + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate; + type = dbm.dataType; + seed = seedLink; + Promise = options.Promise; +}; + +exports.up = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200407175551-create-case-data-table-up.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports.down = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200407175551-create-case-data-table-down.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports._meta = { + "version": 1 +}; diff --git a/migrations/20200415141342-add-model-runs-to-simulation-runs.js b/migrations/20200415141342-add-model-runs-to-simulation-runs.js new file mode 100644 index 0000000..76fd197 --- /dev/null +++ b/migrations/20200415141342-add-model-runs-to-simulation-runs.js @@ -0,0 +1,53 @@ +'use strict'; + +var dbm; +var type; +var seed; +var fs = require('fs'); +var path = require('path'); +var Promise; + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate; + type = dbm.dataType; + seed = seedLink; + Promise = options.Promise; +}; + +exports.up = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200415141342-add-model-runs-to-simulation-runs-up.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports.down = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200415141342-add-model-runs-to-simulation-runs-down.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports._meta = { + "version": 1 +}; diff --git a/migrations/20200416174456-add-admin-to-authorized-users.js b/migrations/20200416174456-add-admin-to-authorized-users.js new file mode 100644 index 0000000..cbfa525 --- /dev/null +++ b/migrations/20200416174456-add-admin-to-authorized-users.js @@ -0,0 +1,53 @@ +'use strict'; + +var dbm; +var type; +var seed; +var fs = require('fs'); +var path = require('path'); +var Promise; + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate; + type = dbm.dataType; + seed = seedLink; + Promise = options.Promise; +}; + +exports.up = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200416174456-add-admin-to-authorized-users-up.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports.down = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200416174456-add-admin-to-authorized-users-down.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports._meta = { + "version": 1 +}; diff --git a/migrations/20200421201526-add-config-to-authorized-users.js b/migrations/20200421201526-add-config-to-authorized-users.js new file mode 100644 index 0000000..d9f6dfb --- /dev/null +++ b/migrations/20200421201526-add-config-to-authorized-users.js @@ -0,0 +1,53 @@ +'use strict'; + +var dbm; +var type; +var seed; +var fs = require('fs'); +var path = require('path'); +var Promise; + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate; + type = dbm.dataType; + seed = seedLink; + Promise = options.Promise; +}; + +exports.up = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200421201526-add-config-to-authorized-users-up.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports.down = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200421201526-add-config-to-authorized-users-down.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports._meta = { + "version": 1 +}; diff --git a/migrations/20200422153859-add-label-to-simulation-runs.js b/migrations/20200422153859-add-label-to-simulation-runs.js new file mode 100644 index 0000000..ec45305 --- /dev/null +++ b/migrations/20200422153859-add-label-to-simulation-runs.js @@ -0,0 +1,59 @@ +'use strict' + +var dbm +var type +var seed +var fs = require('fs') +var path = require('path') +var Promise + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate + type = dbm.dataType + seed = seedLink + Promise = options.Promise +} + +exports.up = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200422153859-add-label-to-simulation-runs-up.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports.down = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200422153859-add-label-to-simulation-runs-down.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports._meta = { + version: 1 +} diff --git a/migrations/20200427195151-create-intervention-data-table.js b/migrations/20200427195151-create-intervention-data-table.js new file mode 100644 index 0000000..decd757 --- /dev/null +++ b/migrations/20200427195151-create-intervention-data-table.js @@ -0,0 +1,56 @@ +'use strict' + +const path = require('path') +const fs = require('fs') + +var dbm +var type +var seed + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate + type = dbm.dataType + seed = seedLink +} + +exports.up = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200427195151-create-intervention-data-table-up.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports.down = function(db) { + var filePath = path.join( + __dirname, + 'sqls', + '20200427195151-create-intervention-data-table-down.sql' + ) + return new Promise(function(resolve, reject) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err, data) { + if (err) return reject(err) + console.log('received data: ' + data) + resolve(data) + }) + }).then(function(data) { + return db.runSql(data) + }) +} + +exports._meta = { + version: 1 +} diff --git a/migrations/20200430164001-add-new-europe-regions.js b/migrations/20200430164001-add-new-europe-regions.js new file mode 100644 index 0000000..47b36bd --- /dev/null +++ b/migrations/20200430164001-add-new-europe-regions.js @@ -0,0 +1,53 @@ +'use strict'; + +var dbm; +var type; +var seed; +var fs = require('fs'); +var path = require('path'); +var Promise; + +/** + * We receive the dbmigrate dependency from dbmigrate initially. + * This enables us to not have to rely on NODE_PATH. + */ +exports.setup = function(options, seedLink) { + dbm = options.dbmigrate; + type = dbm.dataType; + seed = seedLink; + Promise = options.Promise; +}; + +exports.up = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200430164001-add-new-europe-regions-up.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports.down = function(db) { + var filePath = path.join(__dirname, 'sqls', '20200430164001-add-new-europe-regions-down.sql'); + return new Promise( function( resolve, reject ) { + fs.readFile(filePath, {encoding: 'utf-8'}, function(err,data){ + if (err) return reject(err); + console.log('received data: ' + data); + + resolve(data); + }); + }) + .then(function(data) { + return db.runSql(data); + }); +}; + +exports._meta = { + "version": 1 +}; diff --git a/migrations/sqls/20200331170118-create-simulations-runs-table-down.sql b/migrations/sqls/20200331170118-create-simulations-runs-table-down.sql new file mode 100644 index 0000000..e416643 --- /dev/null +++ b/migrations/sqls/20200331170118-create-simulations-runs-table-down.sql @@ -0,0 +1 @@ +DROP TABLE simulation_runs; diff --git a/migrations/sqls/20200331170118-create-simulations-runs-table-up.sql b/migrations/sqls/20200331170118-create-simulations-runs-table-up.sql new file mode 100644 index 0000000..ada4fd7 --- /dev/null +++ b/migrations/sqls/20200331170118-create-simulations-runs-table-up.sql @@ -0,0 +1,22 @@ +CREATE TABLE simulation_runs( + id INT AUTO_INCREMENT PRIMARY KEY, + + # The location ID of the run + location_id INT NOT NULL, + + # The current run status + status VARCHAR(64) NOT NULL, + + # The ID of the user that prompted the run + github_user_id INT NOT NULL, + + # The configuration of the run + configuration JSON NOT NULL, + + # A URL pointing to the results in blob storage + results_data TEXT, + + # Inserted/updated metadata + created_at DATETIME NOT NULL, + updated_at DATETIME NOT NULL +); diff --git a/migrations/sqls/20200331210801-create-locations-table-down.sql b/migrations/sqls/20200331210801-create-locations-table-down.sql new file mode 100644 index 0000000..e127c0d --- /dev/null +++ b/migrations/sqls/20200331210801-create-locations-table-down.sql @@ -0,0 +1 @@ +DROP TABLE locations; diff --git a/migrations/sqls/20200331210801-create-locations-table-up.sql b/migrations/sqls/20200331210801-create-locations-table-up.sql new file mode 100644 index 0000000..3cfead5 --- /dev/null +++ b/migrations/sqls/20200331210801-create-locations-table-up.sql @@ -0,0 +1,12 @@ +CREATE TABLE locations( + id INT AUTO_INCREMENT PRIMARY KEY, + location_id INT NOT NULL, + location_name TEXT NOT NULL, + level INT NOT NULL, + parent_id INT NOT NULL, + path_to_top_parent TEXT NOT NULL, + location_ascii_name TEXT NOT NULL, + location_name_short TEXT NOT NULL, + location_type_id INT NOT NULL, + location_type VARCHAR(32) NOT NULL +); diff --git a/migrations/sqls/20200331233621-add-github-user-login-to-simulation-runs-down.sql b/migrations/sqls/20200331233621-add-github-user-login-to-simulation-runs-down.sql new file mode 100644 index 0000000..386dcd6 --- /dev/null +++ b/migrations/sqls/20200331233621-add-github-user-login-to-simulation-runs-down.sql @@ -0,0 +1 @@ +ALTER TABLE simulation_runs DROP COLUMN github_user_login diff --git a/migrations/sqls/20200331233621-add-github-user-login-to-simulation-runs-up.sql b/migrations/sqls/20200331233621-add-github-user-login-to-simulation-runs-up.sql new file mode 100644 index 0000000..2f42d00 --- /dev/null +++ b/migrations/sqls/20200331233621-add-github-user-login-to-simulation-runs-up.sql @@ -0,0 +1 @@ +ALTER TABLE simulation_runs ADD COLUMN github_user_login VARCHAR(40) diff --git a/migrations/sqls/20200402165609-drop-location-id-from-simulation-runs-down.sql b/migrations/sqls/20200402165609-drop-location-id-from-simulation-runs-down.sql new file mode 100644 index 0000000..649e715 --- /dev/null +++ b/migrations/sqls/20200402165609-drop-location-id-from-simulation-runs-down.sql @@ -0,0 +1 @@ +ALTER TABLE simulation_runs ADD COLUMN location_id INT NOT NULL diff --git a/migrations/sqls/20200402165609-drop-location-id-from-simulation-runs-up.sql b/migrations/sqls/20200402165609-drop-location-id-from-simulation-runs-up.sql new file mode 100644 index 0000000..f74cb43 --- /dev/null +++ b/migrations/sqls/20200402165609-drop-location-id-from-simulation-runs-up.sql @@ -0,0 +1 @@ +ALTER TABLE simulation_runs DROP COLUMN location_id; diff --git a/migrations/sqls/20200402165728-create-regions-table-down.sql b/migrations/sqls/20200402165728-create-regions-table-down.sql new file mode 100644 index 0000000..31c106f --- /dev/null +++ b/migrations/sqls/20200402165728-create-regions-table-down.sql @@ -0,0 +1 @@ +DROP TABLE regions; diff --git a/migrations/sqls/20200402165728-create-regions-table-up.sql b/migrations/sqls/20200402165728-create-regions-table-up.sql new file mode 100644 index 0000000..41a7bc1 --- /dev/null +++ b/migrations/sqls/20200402165728-create-regions-table-up.sql @@ -0,0 +1,9 @@ +CREATE TABLE regions( + id VARCHAR(32) PRIMARY KEY, + name TEXT NOT NULL, + parent_id VARCHAR(32), + created_at DATETIME NOT NULL, + updated_at DATETIME NOT NULL, + + FOREIGN KEY (parent_id) REFERENCES regions(id) ON DELETE CASCADE +) diff --git a/migrations/sqls/20200402165838-add-iso-region-columns-to-simulation-runs-down.sql b/migrations/sqls/20200402165838-add-iso-region-columns-to-simulation-runs-down.sql new file mode 100644 index 0000000..52cbc5f --- /dev/null +++ b/migrations/sqls/20200402165838-add-iso-region-columns-to-simulation-runs-down.sql @@ -0,0 +1,5 @@ +ALTER TABLE simulation_runs + DROP FOREIGN KEY simulation_runs_ibfk_1, + DROP FOREIGN KEY simulation_runs_ibfk_2, + DROP COLUMN region_id, + DROP COLUMN subregion_id; diff --git a/migrations/sqls/20200402165838-add-iso-region-columns-to-simulation-runs-up.sql b/migrations/sqls/20200402165838-add-iso-region-columns-to-simulation-runs-up.sql new file mode 100644 index 0000000..82619c3 --- /dev/null +++ b/migrations/sqls/20200402165838-add-iso-region-columns-to-simulation-runs-up.sql @@ -0,0 +1,7 @@ +ALTER TABLE simulation_runs + ADD region_id VARCHAR(32), + ADD subregion_id VARCHAR(32), + ADD FOREIGN KEY (region_id) REFERENCES regions(id) ON DELETE RESTRICT, + ADD FOREIGN KEY (subregion_id) REFERENCES regions(id) ON DELETE RESTRICT, + ADD INDEX (region_id), + ADD INDEX (subregion_id); diff --git a/migrations/sqls/20200402172411-drop-locations-table-down.sql b/migrations/sqls/20200402172411-drop-locations-table-down.sql new file mode 100644 index 0000000..3cfead5 --- /dev/null +++ b/migrations/sqls/20200402172411-drop-locations-table-down.sql @@ -0,0 +1,12 @@ +CREATE TABLE locations( + id INT AUTO_INCREMENT PRIMARY KEY, + location_id INT NOT NULL, + location_name TEXT NOT NULL, + level INT NOT NULL, + parent_id INT NOT NULL, + path_to_top_parent TEXT NOT NULL, + location_ascii_name TEXT NOT NULL, + location_name_short TEXT NOT NULL, + location_type_id INT NOT NULL, + location_type VARCHAR(32) NOT NULL +); diff --git a/migrations/sqls/20200402172411-drop-locations-table-up.sql b/migrations/sqls/20200402172411-drop-locations-table-up.sql new file mode 100644 index 0000000..e127c0d --- /dev/null +++ b/migrations/sqls/20200402172411-drop-locations-table-up.sql @@ -0,0 +1 @@ +DROP TABLE locations; diff --git a/migrations/sqls/20200402181839-insert-default-region-down.sql b/migrations/sqls/20200402181839-insert-default-region-down.sql new file mode 100644 index 0000000..36a0aca --- /dev/null +++ b/migrations/sqls/20200402181839-insert-default-region-down.sql @@ -0,0 +1 @@ +DELETE FROM regions WHERE id = 'GB'; diff --git a/migrations/sqls/20200402181839-insert-default-region-up.sql b/migrations/sqls/20200402181839-insert-default-region-up.sql new file mode 100644 index 0000000..1cce71a --- /dev/null +++ b/migrations/sqls/20200402181839-insert-default-region-up.sql @@ -0,0 +1 @@ +INSERT INTO regions (id, name, created_at, updated_at) VALUES ('GB', 'United Kingdom', NOW(), NOW()); diff --git a/migrations/sqls/20200404153055-add-workflow-run-id-to-simulation-runs-down.sql b/migrations/sqls/20200404153055-add-workflow-run-id-to-simulation-runs-down.sql new file mode 100644 index 0000000..723217a --- /dev/null +++ b/migrations/sqls/20200404153055-add-workflow-run-id-to-simulation-runs-down.sql @@ -0,0 +1 @@ +ALTER TABLE simulation_runs DROP workflow_run_id; diff --git a/migrations/sqls/20200404153055-add-workflow-run-id-to-simulation-runs-up.sql b/migrations/sqls/20200404153055-add-workflow-run-id-to-simulation-runs-up.sql new file mode 100644 index 0000000..77d39c6 --- /dev/null +++ b/migrations/sqls/20200404153055-add-workflow-run-id-to-simulation-runs-up.sql @@ -0,0 +1 @@ +ALTER TABLE simulation_runs ADD workflow_run_id INT; diff --git a/migrations/sqls/20200406164833-add-github-user-id-index-to-simulation-runs-down.sql b/migrations/sqls/20200406164833-add-github-user-id-index-to-simulation-runs-down.sql new file mode 100644 index 0000000..4aff278 --- /dev/null +++ b/migrations/sqls/20200406164833-add-github-user-id-index-to-simulation-runs-down.sql @@ -0,0 +1 @@ +ALTER TABLE simulation_runs DROP INDEX github_user_id; diff --git a/migrations/sqls/20200406164833-add-github-user-id-index-to-simulation-runs-up.sql b/migrations/sqls/20200406164833-add-github-user-id-index-to-simulation-runs-up.sql new file mode 100644 index 0000000..7bc83c4 --- /dev/null +++ b/migrations/sqls/20200406164833-add-github-user-id-index-to-simulation-runs-up.sql @@ -0,0 +1 @@ +ALTER TABLE simulation_runs ADD INDEX (github_user_id); diff --git a/migrations/sqls/20200406180709-rename-uk-to-gb-down.sql b/migrations/sqls/20200406180709-rename-uk-to-gb-down.sql new file mode 100644 index 0000000..fc73ec6 --- /dev/null +++ b/migrations/sqls/20200406180709-rename-uk-to-gb-down.sql @@ -0,0 +1 @@ +UPDATE regions SET name = 'United Kingdom' WHERE id = 'GB'; diff --git a/migrations/sqls/20200406180709-rename-uk-to-gb-up.sql b/migrations/sqls/20200406180709-rename-uk-to-gb-up.sql new file mode 100644 index 0000000..cf8b63b --- /dev/null +++ b/migrations/sqls/20200406180709-rename-uk-to-gb-up.sql @@ -0,0 +1 @@ +UPDATE regions SET name = 'Great Britain' WHERE id = 'GB'; diff --git a/migrations/sqls/20200406183238-create-authorized-users-down.sql b/migrations/sqls/20200406183238-create-authorized-users-down.sql new file mode 100644 index 0000000..6f791e3 --- /dev/null +++ b/migrations/sqls/20200406183238-create-authorized-users-down.sql @@ -0,0 +1 @@ +DROP TABLE authorized_users; diff --git a/migrations/sqls/20200406183238-create-authorized-users-up.sql b/migrations/sqls/20200406183238-create-authorized-users-up.sql new file mode 100644 index 0000000..2878b8d --- /dev/null +++ b/migrations/sqls/20200406183238-create-authorized-users-up.sql @@ -0,0 +1,6 @@ +CREATE TABLE authorized_users( + id INT AUTO_INCREMENT PRIMARY KEY, + github_user_login VARCHAR(40) UNIQUE NOT NULL, + created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP, + updated_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP +); diff --git a/migrations/sqls/20200406191215-insert-us-subregions-down.sql b/migrations/sqls/20200406191215-insert-us-subregions-down.sql new file mode 100644 index 0000000..e18fea3 --- /dev/null +++ b/migrations/sqls/20200406191215-insert-us-subregions-down.sql @@ -0,0 +1 @@ +DELETE FROM regions WHERE id = 'US' OR parent_id = 'US'; diff --git a/migrations/sqls/20200406191215-insert-us-subregions-up.sql b/migrations/sqls/20200406191215-insert-us-subregions-up.sql new file mode 100644 index 0000000..5866d61 --- /dev/null +++ b/migrations/sqls/20200406191215-insert-us-subregions-up.sql @@ -0,0 +1,51 @@ +INSERT INTO regions (id, parent_id, name, created_at, updated_at) VALUES + ('US', NULL, 'United States', NOW(), NOW()), + ('US-AL', 'US', 'Alabama', NOW(), NOW()), + ('US-AZ', 'US', 'Arizona', NOW(), NOW()), + ('US-AR', 'US', 'Arkansas', NOW(), NOW()), + ('US-CA', 'US', 'California', NOW(), NOW()), + ('US-CO', 'US', 'Colorado', NOW(), NOW()), + ('US-CT', 'US', 'Connecticut', NOW(), NOW()), + ('US-DE', 'US', 'Delaware', NOW(), NOW()), + ('US-FL', 'US', 'Florida', NOW(), NOW()), + ('US-GA', 'US', 'Georgia', NOW(), NOW()), + ('US-ID', 'US', 'Idaho', NOW(), NOW()), + ('US-IL', 'US', 'Illinois', NOW(), NOW()), + ('US-IN', 'US', 'Indiana', NOW(), NOW()), + ('US-IA', 'US', 'Iowa', NOW(), NOW()), + ('US-KS', 'US', 'Kansas', NOW(), NOW()), + ('US-KY', 'US', 'Kentucky', NOW(), NOW()), + ('US-LA', 'US', 'Louisiana', NOW(), NOW()), + ('US-ME', 'US', 'Maine', NOW(), NOW()), + ('US-MD', 'US', 'Maryland', NOW(), NOW()), + ('US-MA', 'US', 'Massachusetts', NOW(), NOW()), + ('US-MI', 'US', 'Michigan', NOW(), NOW()), + ('US-MN', 'US', 'Minnesota', NOW(), NOW()), + ('US-MS', 'US', 'Mississippi', NOW(), NOW()), + ('US-MO', 'US', 'Missouri', NOW(), NOW()), + ('US-MT', 'US', 'Montana', NOW(), NOW()), + ('US-NE', 'US', 'Nebraska', NOW(), NOW()), + ('US-NV', 'US', 'Nevada', NOW(), NOW()), + ('US-NH', 'US', 'New Hampshire', NOW(), NOW()), + ('US-NJ', 'US', 'New Jersey', NOW(), NOW()), + ('US-NM', 'US', 'New Mexico', NOW(), NOW()), + ('US-NY', 'US', 'New York', NOW(), NOW()), + ('US-NC', 'US', 'North Carolina', NOW(), NOW()), + ('US-ND', 'US', 'North Dakota', NOW(), NOW()), + ('US-OH', 'US', 'Ohio', NOW(), NOW()), + ('US-OK', 'US', 'Oklahoma', NOW(), NOW()), + ('US-OR', 'US', 'Oregon', NOW(), NOW()), + ('US-PA', 'US', 'Pennsylvania', NOW(), NOW()), + ('US-RI', 'US', 'Rhode Island', NOW(), NOW()), + ('US-SC', 'US', 'South Carolina', NOW(), NOW()), + ('US-SD', 'US', 'South Dakota', NOW(), NOW()), + ('US-TN', 'US', 'Tennessee', NOW(), NOW()), + ('US-TX', 'US', 'Texas', NOW(), NOW()), + ('US-UT', 'US', 'Utah', NOW(), NOW()), + ('US-VT', 'US', 'Vermont', NOW(), NOW()), + ('US-VA', 'US', 'Virginia', NOW(), NOW()), + ('US-WA', 'US', 'Washington', NOW(), NOW()), + ('US-WV', 'US', 'West Virginia', NOW(), NOW()), + ('US-WI', 'US', 'Wisconsin', NOW(), NOW()), + ('US-WY', 'US', 'Wyoming', NOW(), NOW()), + ('US-DC', 'US', 'District of Columbia', NOW(), NOW()); diff --git a/migrations/sqls/20200406222239-insert-ak-hi-down.sql b/migrations/sqls/20200406222239-insert-ak-hi-down.sql new file mode 100644 index 0000000..1713786 --- /dev/null +++ b/migrations/sqls/20200406222239-insert-ak-hi-down.sql @@ -0,0 +1 @@ +DELETE FROM regions WHERE id IN ('US-AK', 'US-HI'); diff --git a/migrations/sqls/20200406222239-insert-ak-hi-up.sql b/migrations/sqls/20200406222239-insert-ak-hi-up.sql new file mode 100644 index 0000000..7daf7b1 --- /dev/null +++ b/migrations/sqls/20200406222239-insert-ak-hi-up.sql @@ -0,0 +1,3 @@ +INSERT INTO regions (id, parent_id, name, created_at, updated_at) VALUES + ('US-AK', 'US', 'Alaska', NOW(), NOW()), + ('US-HI', 'US', 'Hawaii', NOW(), NOW()); diff --git a/migrations/sqls/20200407175551-create-case-data-table-down.sql b/migrations/sqls/20200407175551-create-case-data-table-down.sql new file mode 100644 index 0000000..05869a6 --- /dev/null +++ b/migrations/sqls/20200407175551-create-case-data-table-down.sql @@ -0,0 +1 @@ +DROP TABLE case_data diff --git a/migrations/sqls/20200407175551-create-case-data-table-up.sql b/migrations/sqls/20200407175551-create-case-data-table-up.sql new file mode 100644 index 0000000..7feaf5e --- /dev/null +++ b/migrations/sqls/20200407175551-create-case-data-table-up.sql @@ -0,0 +1,14 @@ +CREATE TABLE case_data( + id INT AUTO_INCREMENT PRIMARY KEY, + region_id VARCHAR(32) NOT NULL, + subregion_id VARCHAR(32), + date DATE NOT NULL, + confirmed INT NOT NULL, + recovered INT NOT NULL, + deaths INT NOT NULL, + created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP, + updated_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP, + INDEX (region_id), + INDEX (subregion_id), + UNIQUE INDEX (region_id, subregion_id, date) +) diff --git a/migrations/sqls/20200415141342-add-model-runs-to-simulation-runs-down.sql b/migrations/sqls/20200415141342-add-model-runs-to-simulation-runs-down.sql new file mode 100644 index 0000000..f70f6ab --- /dev/null +++ b/migrations/sqls/20200415141342-add-model-runs-to-simulation-runs-down.sql @@ -0,0 +1,21 @@ +ALTER TABLE simulation_runs + ADD results_data TEXT, + ADD status VARCHAR(64); + +UPDATE simulation_runs + SET + results_data = IF( + JSON_TYPE(simulation_runs.model_runs->'$[0].results_data') = 'NULL', + NULL, + IF( + simulation_runs.model_runs->>'$[0].results_data' = '', + NULL, + simulation_runs.model_runs->>'$[0].results_data')), + status = simulation_runs.model_runs->>'$[0].status'; + +ALTER TABLE simulation_runs + CHANGE status status VARCHAR(64) NOT NULL; + +ALTER TABLE simulation_runs + DROP model_runs; + diff --git a/migrations/sqls/20200415141342-add-model-runs-to-simulation-runs-up.sql b/migrations/sqls/20200415141342-add-model-runs-to-simulation-runs-up.sql new file mode 100644 index 0000000..eb4e6cc --- /dev/null +++ b/migrations/sqls/20200415141342-add-model-runs-to-simulation-runs-up.sql @@ -0,0 +1,14 @@ +ALTER TABLE simulation_runs ADD model_runs JSON; + +UPDATE simulation_runs + SET model_runs = JSON_ARRAY(JSON_OBJECT( + 'model_slug', 'mrc-ide-covid-sim', + 'status', simulation_runs.status, + 'results_data', simulation_runs.results_data)); + +ALTER TABLE simulation_runs + DROP status, + DROP results_data; + +ALTER TABLE simulation_runs + CHANGE model_runs model_runs JSON NOT NULL; diff --git a/migrations/sqls/20200416174456-add-admin-to-authorized-users-down.sql b/migrations/sqls/20200416174456-add-admin-to-authorized-users-down.sql new file mode 100644 index 0000000..76b0966 --- /dev/null +++ b/migrations/sqls/20200416174456-add-admin-to-authorized-users-down.sql @@ -0,0 +1 @@ +ALTER TABLE authorized_users DROP admin; diff --git a/migrations/sqls/20200416174456-add-admin-to-authorized-users-up.sql b/migrations/sqls/20200416174456-add-admin-to-authorized-users-up.sql new file mode 100644 index 0000000..8fa8f19 --- /dev/null +++ b/migrations/sqls/20200416174456-add-admin-to-authorized-users-up.sql @@ -0,0 +1 @@ +ALTER TABLE authorized_users ADD admin BOOLEAN DEFAULT FALSE; diff --git a/migrations/sqls/20200421201526-add-config-to-authorized-users-down.sql b/migrations/sqls/20200421201526-add-config-to-authorized-users-down.sql new file mode 100644 index 0000000..9a90573 --- /dev/null +++ b/migrations/sqls/20200421201526-add-config-to-authorized-users-down.sql @@ -0,0 +1 @@ +ALTER TABLE authorized_users DROP config; diff --git a/migrations/sqls/20200421201526-add-config-to-authorized-users-up.sql b/migrations/sqls/20200421201526-add-config-to-authorized-users-up.sql new file mode 100644 index 0000000..5eb044c --- /dev/null +++ b/migrations/sqls/20200421201526-add-config-to-authorized-users-up.sql @@ -0,0 +1 @@ +ALTER TABLE authorized_users ADD config JSON NOT NULL DEFAULT (JSON_OBJECT()); diff --git a/migrations/sqls/20200422153859-add-label-to-simulation-runs-down.sql b/migrations/sqls/20200422153859-add-label-to-simulation-runs-down.sql new file mode 100644 index 0000000..951155e --- /dev/null +++ b/migrations/sqls/20200422153859-add-label-to-simulation-runs-down.sql @@ -0,0 +1 @@ +ALTER TABLE simulation_runs DROP label; diff --git a/migrations/sqls/20200422153859-add-label-to-simulation-runs-up.sql b/migrations/sqls/20200422153859-add-label-to-simulation-runs-up.sql new file mode 100644 index 0000000..40ea023 --- /dev/null +++ b/migrations/sqls/20200422153859-add-label-to-simulation-runs-up.sql @@ -0,0 +1 @@ +ALTER TABLE simulation_runs ADD label TEXT NOT NULL; diff --git a/migrations/sqls/20200427195151-create-intervention-data-table-down.sql b/migrations/sqls/20200427195151-create-intervention-data-table-down.sql new file mode 100644 index 0000000..5d576a1 --- /dev/null +++ b/migrations/sqls/20200427195151-create-intervention-data-table-down.sql @@ -0,0 +1 @@ +DROP TABLE intervention_data diff --git a/migrations/sqls/20200427195151-create-intervention-data-table-up.sql b/migrations/sqls/20200427195151-create-intervention-data-table-up.sql new file mode 100644 index 0000000..f70597d --- /dev/null +++ b/migrations/sqls/20200427195151-create-intervention-data-table-up.sql @@ -0,0 +1,17 @@ +CREATE TABLE intervention_data( + id INT AUTO_INCREMENT PRIMARY KEY, + region_id VARCHAR(32) NOT NULL, + subregion_id VARCHAR(32), + policy VARCHAR(255) NOT NULL, + notes TEXT, + source TEXT, + issue_date DATE, + start_date DATE NOT NULL, + ease_date DATE, + expiration_date DATE, + end_date DATE, + created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP, + updated_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP, + INDEX (region_id), + INDEX (subregion_id) +) diff --git a/migrations/sqls/20200430164001-add-new-europe-regions-down.sql b/migrations/sqls/20200430164001-add-new-europe-regions-down.sql new file mode 100644 index 0000000..b5c0a3c --- /dev/null +++ b/migrations/sqls/20200430164001-add-new-europe-regions-down.sql @@ -0,0 +1,42 @@ +DELETE FROM regions WHERE id IN ( + 'AT', + 'AL', + 'BY', + 'BE', + 'BA', + 'BG', + 'CA', + 'HR', + 'CR', + 'DK', + 'EE', + 'FI', + 'FR', + 'DE', + 'GI', + 'GR', + 'HU', + 'IS', + 'IR', + 'IT', + 'LV', + 'LT', + 'LU', + 'MK', + 'MT', + 'MD', + 'ME', + 'NL', + 'NO', + 'PT', + 'PL', + 'RO', + 'RU', + 'RS', + 'SK', + 'SI', + 'ES', + 'SE', + 'CH', + 'UA' +); diff --git a/migrations/sqls/20200430164001-add-new-europe-regions-up.sql b/migrations/sqls/20200430164001-add-new-europe-regions-up.sql new file mode 100644 index 0000000..ae9b147 --- /dev/null +++ b/migrations/sqls/20200430164001-add-new-europe-regions-up.sql @@ -0,0 +1,41 @@ +INSERT INTO regions (id, parent_id, name, created_at, updated_at) VALUES + ('AT', NULL, 'Austria', NOW(), NOW()), + ('AL', NULL, 'Albania', NOW(), NOW()), + ('BY', NULL, 'Belarus', NOW(), NOW()), + ('BE', NULL, 'Belgium', NOW(), NOW()), + ('BA', NULL, 'Bosnia and Herzegovina', NOW(), NOW()), + ('BG', NULL, 'Bulgaria', NOW(), NOW()), + ('CA', NULL, 'Canada', NOW(), NOW()), + ('HR', NULL, 'Croatia', NOW(), NOW()), + ('CR', NULL, 'Czechia', NOW(), NOW()), + ('DK', NULL, 'Denmark', NOW(), NOW()), + ('EE', NULL, 'Estonia', NOW(), NOW()), + ('FI', NULL, 'Finland', NOW(), NOW()), + ('FR', NULL, 'France', NOW(), NOW()), + ('DE', NULL, 'Germany', NOW(), NOW()), + ('GI', NULL, 'Gibraltar', NOW(), NOW()), + ('GR', NULL, 'Greece', NOW(), NOW()), + ('HU', NULL, 'Hungary', NOW(), NOW()), + ('IS', NULL, 'Iceland', NOW(), NOW()), + ('IR', NULL, 'Ireland', NOW(), NOW()), + ('IT', NULL, 'Italy', NOW(), NOW()), + ('LV', NULL, 'Latvia', NOW(), NOW()), + ('LT', NULL, 'Lithuania', NOW(), NOW()), + ('LU', NULL, 'Luxembourg', NOW(), NOW()), + ('MK', NULL, 'Republic of North Macedonia', NOW(), NOW()), + ('MT', NULL, 'Malta', NOW(), NOW()), + ('MD', NULL, 'Moldova', NOW(), NOW()), + ('ME', NULL, 'Montenegro', NOW(), NOW()), + ('NL', NULL, 'Netherlands', NOW(), NOW()), + ('NO', NULL, 'Norway', NOW(), NOW()), + ('PT', NULL, 'Portugal', NOW(), NOW()), + ('PL', NULL, 'Poland', NOW(), NOW()), + ('RO', NULL, 'Romania', NOW(), NOW()), + ('RU', NULL, 'Russian Federation', NOW(), NOW()), + ('RS', NULL, 'Serbia', NOW(), NOW()), + ('SK', NULL, 'Slovakia', NOW(), NOW()), + ('SI', NULL, 'Slovenia', NOW(), NOW()), + ('ES', NULL, 'Spain', NOW(), NOW()), + ('SE', NULL, 'Sweden', NOW(), NOW()), + ('CH', NULL, 'Switzerland', NOW(), NOW()), + ('UA', NULL, 'Ukraine', NOW(), NOW()); diff --git a/models.yml b/models.yml new file mode 100644 index 0000000..ead91e4 --- /dev/null +++ b/models.yml @@ -0,0 +1,55 @@ +basel: + name: Covid19-Scenarios (Neher) + origin: Neher Lab, Biozentrum Basel + isProductionReady: true + imageURL: docker.pkg.github.com/covid-modeling/model-runner/neherlab-covid-19-scenarios-connector:0.9.1 + metaURLs: + code: https://github.com/neherlab/covid19_scenarios + website: https://covid19-scenarios.org/about + description: | + We implement an age-stratified SEIR model with additional categories + for individuals exposed to the virus that are not yet infectious, severely sick + people in need of hospitalization, people in critical condition, and a fatal category. + The model is currently under active development and the US state level parameters are under review. + supportedParameters: + - contactReduction + - r0 + +mrc-ide-covid-sim: + name: CovidSim (Imperial) + origin: Imperial College + isProductionReady: true + imageURL: docker.pkg.github.com/covid-modeling/model-runner/mrc-ide-covidsim-connector:0.9.2 + metaURLs: + code: https://github.com/mrc-ide/covid-sim + paper: https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-College-COVID19-NPI-modelling-16-03-2020.pdf + description: | + We consider the feasibility and implications of strategies for COVID-19, + looking at a range of NPI measures. It is important to note at the outset + that given SARS-CoV-2 is a newly emergent virus, much remains to be + understood about its transmission. In addition, the impact of many of the + NPIs detailed here depends critically on how people respond to their + introduction, which is highly likely to vary between countries and even + communities. + supportedParameters: + - interventionStrategies + - r0 + +mc19: + name: Modeling Covid-19 + origin: Modeling Covid-19 + imageURL: docker.pkg.github.com/covid-modeling/model-runner/modelingcovid-covidmodel-connector:0.3.0 + isProductionReady: false + metaURLs: + code: https://github.com/modelingcovid/covidmodel + paper: https://dash.harvard.edu/bitstream/handle/1/42638988/Social%20distancing%20strategies%20for%20curbing%20the%20Covid-19%20epidemic.pdf?sequence=1&isAllowed=y + website: https://covidmodel-flax.now.sh/about + description: | + We’ve implemented a model for the spread of the virus which is an enrichment + of the basic SEIR model with adjustments for distancing and adding PCR confirmation + and Fatality states. This allows us to fit the solutions of the system of SEIR equations + to actual data as reported by various states. We then use a combination of parameters + from the fits and literature values to generate Monte Carlo simulations around the + fit expectations to get a sense of our uncertainty in the projections. + supportedParameters: + - contactReduction diff --git a/next-env.d.ts b/next-env.d.ts new file mode 100644 index 0000000..7b7aa2c --- /dev/null +++ b/next-env.d.ts @@ -0,0 +1,2 @@ +/// +/// diff --git a/next.config.js b/next.config.js new file mode 100644 index 0000000..5725c40 --- /dev/null +++ b/next.config.js @@ -0,0 +1,80 @@ +const {DefinePlugin} = require('webpack') + +// This garbage is just to fix intellisense for the import. +const sentryPluginImport = /** @type {any} */ (require('@sentry/webpack-plugin')) +/** @type {typeof import('@sentry/webpack-plugin').default} */ +const SentryWebpackPlugin = sentryPluginImport + +module.exports = { + env: { + GITHUB_CLIENT_ID: process.env.GITHUB_CLIENT_ID, + SENTRY_DSN: process.env.SENTRY_DSN, + APP_ENVIRONMENT: process.env.APP_ENVIRONMENT + }, + + webpack: (config, options) => { + const commit = process.env.NOW_GITHUB_COMMIT_SHA || process.env.GITHUB_SHA + const release = commit || options.buildId + + config.module.rules.push({ + test: /\.ya?ml$/, + use: 'js-yaml-loader' + }) + + config.plugins.push( + new DefinePlugin({ + 'process.env.SENTRY_RELEASE': `"${release}"` + }) + ) + + config = nextSourceMaps(config, options) + + const releaseInfo = { + release, + repo: 'covid-modeling/web', + commit + } + + console.log('Configuring Sentry release:', JSON.stringify(releaseInfo)) + + if (process.env.NODE_ENV === 'production') { + config.plugins.push( + new SentryWebpackPlugin({ + include: ['.', '.next'], + ignore: ['migrations', 'node_modules'], + ...releaseInfo + }) + ) + } + + if (!options.isServer) { + config.resolve.alias['@sentry/node'] = '@sentry/browser' + } + + return config + } +} + +function nextSourceMaps(config, options) { + if (!options.dev) { + config.devtool = 'source-map' + + for (const plugin of config.plugins) { + if (plugin.constructor.name === 'UglifyJsPlugin') { + plugin.options.sourceMap = true + break + } + } + + if (config.optimization && config.optimization.minimizer) { + for (const plugin of config.optimization.minimizer) { + if (plugin.constructor.name === 'TerserPlugin') { + plugin.options.sourceMap = true + break + } + } + } + } + + return config +} diff --git a/now.json b/now.json new file mode 100644 index 0000000..9c96808 --- /dev/null +++ b/now.json @@ -0,0 +1,38 @@ +{ + "regions": ["iad1"], + "alias": "staging.covid-modeling.org", + "build": { + "env": { + "BLOB_STORAGE_ACCOUNT": "@staging-blob-storage-account", + "BLOB_STORAGE_CONTAINER": "@staging-blob-storage-container", + "BLOB_STORAGE_KEY": "@staging-blob-storage-key", + "GITHUB_CLIENT_ID": "@staging-github-client-id", + "SENTRY_DSN": "@prod-sentry-dsn", + "SENTRY_AUTH_TOKEN": "@prod-sentry-token", + "SENTRY_ORG": "github-disease-modelling", + "SENTRY_PROJECT": "web-api-ui", + "APP_ENVIRONMENT": "staging", + "SESSION_SECRET": "@staging-session-secret" + } + }, + "env": { + "GITHUB_CLIENT_ID": "@staging-github-client-id", + "GITHUB_CLIENT_SECRET": "@staging-github-client-secret", + "GITHUB_API_TOKEN": "@prod-github-api-token", + "CONTROL_REPO_NWO": "covid-modeling/staging-covid19-control-plane", + "CONTROL_REPO_EVENT_TYPE": "run-simulation", + "DB_USERNAME": "@staging-mysql-username", + "DB_PASSWORD": "@staging-mysql-password", + "DB_HOST": "@staging-mysql-host", + "DB_DATABASE": "@staging-mysql-database", + "RUNNER_SHARED_SECRET": "@staging-runner-shared-secret", + "RUNNER_CALLBACK_URL": "https://staging.covid-modeling.org", + "BLOB_STORAGE_ACCOUNT": "@staging-blob-storage-account", + "BLOB_STORAGE_CONTAINER": "@staging-blob-storage-container", + "BLOB_STORAGE_KEY": "@staging-blob-storage-key", + "OAUTH_SECRET": "@staging-oauth-secret", + "SESSION_SECRET": "@staging-session-secret", + "SENTRY_DSN": "@prod-sentry-dsn", + "APP_ENVIRONMENT": "staging" + } +} diff --git a/now.prod.json b/now.prod.json new file mode 100644 index 0000000..64b6067 --- /dev/null +++ b/now.prod.json @@ -0,0 +1,38 @@ +{ + "regions": ["iad1"], + "alias": "covid-modeling.org", + "build": { + "env": { + "BLOB_STORAGE_ACCOUNT": "@prod-blob-storage-account", + "BLOB_STORAGE_CONTAINER": "@prod-blob-storage-container", + "BLOB_STORAGE_KEY": "@prod-blob-storage-key", + "GITHUB_CLIENT_ID": "@prod-github-client-id", + "SENTRY_DSN": "@prod-sentry-dsn", + "SENTRY_AUTH_TOKEN": "@prod-sentry-token", + "SENTRY_ORG": "github-disease-modelling", + "SENTRY_PROJECT": "web-api-ui", + "APP_ENVIRONMENT": "production", + "SESSION_SECRET": "@prod-session-secret" + } + }, + "env": { + "GITHUB_CLIENT_ID": "@prod-github-client-id", + "GITHUB_CLIENT_SECRET": "@prod-github-client-secret", + "GITHUB_API_TOKEN": "@prod-github-api-token", + "CONTROL_REPO_NWO": "covid-modeling/prod-covid19-control-plane", + "CONTROL_REPO_EVENT_TYPE": "run-simulation", + "DB_USERNAME": "@prod-mysql-username", + "DB_PASSWORD": "@prod-mysql-password", + "DB_HOST": "@prod-mysql-host", + "DB_DATABASE": "@prod-mysql-database", + "RUNNER_SHARED_SECRET": "@prod-runner-shared-secret", + "RUNNER_CALLBACK_URL": "https://covid-modeling.org", + "BLOB_STORAGE_ACCOUNT": "@prod-blob-storage-account", + "BLOB_STORAGE_CONTAINER": "@prod-blob-storage-container", + "BLOB_STORAGE_KEY": "@prod-blob-storage-key", + "OAUTH_SECRET": "@prod-oauth-secret", + "SESSION_SECRET": "@prod-session-secret", + "SENTRY_DSN": "@prod-sentry-dsn", + "APP_ENVIRONMENT": "production" + } +} diff --git a/package-lock.json b/package-lock.json new file mode 100644 index 0000000..80f3de3 --- /dev/null +++ b/package-lock.json @@ -0,0 +1,16768 @@ +{ + "requires": true, + "lockfileVersion": 1, + "dependencies": { + "@ampproject/toolbox-core": { + "version": "2.0.0", + "resolved": "https://registry.npmjs.org/@ampproject/toolbox-core/-/toolbox-core-2.0.0.tgz", + "integrity": 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--runInBand --watch --all" + }, + "license": "MIT", + "dependencies": { + "@azure/storage-blob": "^12.1.1", + "@hapi/joi": "^17.1.1", + "@sentry/browser": "^5.15.4", + "@sentry/integrations": "^5.15.4", + "@sentry/node": "^5.15.4", + "axios": "^0.19.2", + "classnames": "^2.2.6", + "cleave.js": "^1.5.10", + "cookies": "^0.8.0", + "d3": "^5.15.0", + "debug": "^4.1.1", + "emoji-flags": "^1.2.0", + "jsonwebtoken": "^8.5.1", + "lodash": "^4.17.15", + "luxon": "^1.22.2", + "next": "^9.3.2", + "numbro": "^2.2.0", + "react": "^16.13.1", + "react-day-picker": "^7.4.0", + "react-dimensions-hook": "^1.0.3", + "react-dom": "^16.13.1", + "react-spring": "^8.0.27", + "react-virtualized": "^9.21.2", + "serverless-mysql": "^1.5.3", + "source-map-support": "^0.5.16", + "sql-template-strings": "^2.2.2", + "swr": "^0.2.0" + }, + "devDependencies": { + "@fullhuman/postcss-purgecss": "^2.1.0", + "@sentry/cli": "^1.52.1", + "@sentry/webpack-plugin": "^1.10.0", + "@types/classnames": "^2.2.10", + 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"@typescript-eslint/no-empty-interface": 1, + "@typescript-eslint/interface-name-prefix": 1, + "@typescript-eslint/no-inferrable-types": 0, + "@typescript-eslint/no-non-null-assertion": 0, + "@typescript-eslint/camelcase": [ + 2, + { + "properties": "never" + } + ], + "@typescript-eslint/no-use-before-define": [ + 2, + { + "functions": false + } + ] + }, + "settings": { + "react": { + "version": "detect" + } + } + }, + "browserslist": { + "production": [ + ">0.2%", + "not dead", + "not op_mini all" + ], + "development": [ + "last 1 chrome version", + "last 1 firefox version", + "last 1 safari version" + ] + }, + "husky": { + "hooks": { + "pre-commit": "npm run lint-staged" + } + }, + "lint-staged": { + "./**/*.{json,css,scss,md}": [ + "prettier --write" + ], + "./**/*.{js,jsx,ts,tsx}": [ + "eslint --fix" + ] + }, + "prettier": { + "singleQuote": true, + "tabWidth": 2, + "semi": false, + "bracketSpacing": false + }, + "bugs": { + "url": "https://github.com/covid-modeling/web/issues", + "email": "covid-modeling+opensource@github.com" + } +} diff --git a/pages/_app.tsx b/pages/_app.tsx new file mode 100644 index 0000000..f58ce92 --- /dev/null +++ b/pages/_app.tsx @@ -0,0 +1,101 @@ +import Axios from 'axios' +import App, {AppContext} from 'next/app' +import NextError from 'next/error' +import Head from 'next/head' +import {createContext} from 'react' +import 'react-day-picker/lib/style.css' +import 'react-virtualized/styles.css' +import {SWRConfig} from 'swr' +import '../css/app.css' +import {initSentry} from '../lib/sentry' + +const {captureContextException, captureException, captureMessage} = initSentry() + +export const SentryContext = createContext<{ + captureException: typeof captureException + captureMessage: typeof captureMessage +}>({captureException, captureMessage}) + +const scriptPolicy = + process.env.NODE_ENV === 'production' + ? // In production builds, only allow JS from within the app. + "'self'" + : // In dev builds, allow JS within the app, + // or the inline scripts bundled by Next.js/webpack in dev mode. + "'self' 'unsafe-inline'" + +const contentSecurityPolicy = [ + `default-src 'none'`, + // Allow JS from within the application and its bundled scripts. + `script-src ${scriptPolicy}`, + // Allow stylesheets within the application or hosted by Google. + // We use inline styles in the React components. + `style-src 'self' https://fonts.googleapis.com 'unsafe-inline'`, + // Allow fonts hosted by Google. + `font-src 'self' https://fonts.googleapis.com https://fonts.gstatic.com`, + // Allow fetch calls to the application's own API, and to Sentry for logging. + `connect-src 'self' https://sentry.io`, + // Allow favicon and other local images. + `img-src 'self'`, + // Prevent the site from being included in an iframe. + `frame-ancestors 'none'`, + // Allow prefetching resources within the application. + `prefetch-src 'self'` +].join('; ') + +/** + * The main application frame. + * + * @param appProps Props provided by Next.js + */ +export default class WebApp extends App { + state: {error?: Error & {statusCode?: number}} = {} + + static async getInitialProps(appContext: AppContext) { + const {ctx} = appContext + + if (ctx.err) { + captureContextException(ctx.err, ctx) + } + + if (ctx.res) { + ctx.res.setHeader('Content-Security-Policy', contentSecurityPolicy) + } + + const pageProps = await App.getInitialProps(appContext) + return {pageProps} + } + + componentDidCatch(err: Error, errorInfo: Record) { + captureException(err, errorInfo) + this.setState({error: err}) + } + + render() { + const {Component, pageProps} = this.props + + if (this.state.error) { + return + } + + return ( + <> + + COVID Modeling + + + + + Axios.get(key).then(resp => resp.data)}} + > + + + + + ) + } +} diff --git a/pages/_document.tsx b/pages/_document.tsx new file mode 100644 index 0000000..6f626bf --- /dev/null +++ b/pages/_document.tsx @@ -0,0 +1,19 @@ +import Document, {Head, Html, Main, NextScript} from 'next/document' +import {catchUnhandledErrors} from '../lib/handle-error' + +catchUnhandledErrors() + +export default class WebDocument extends Document { + render() { + return ( + + + + +

    + + + + ) + } +} diff --git a/pages/about.module.css b/pages/about.module.css new file mode 100644 index 0000000..86b8670 --- /dev/null +++ b/pages/about.module.css @@ -0,0 +1,30 @@ +.AboutPage { + @apply mx-auto; + @apply px-10; + margin-top: 49px; + max-width: 615px; +} + +.AboutPage h1 { + @apply mt-8 mb-4; + @apply font-bold text-3.25xl; +} + +.AboutPage .MainDesc { + @apply mt-8 mb-4; + @apply text-lg; +} + +.AboutPage h2 { + @apply mt-8 mb-4; + @apply font-bold text-lg; +} + +.AboutPage h3 { + @apply mt-8 mb-4; + @apply font-bold; +} + +.AboutPage p { + @apply mt-4; +} diff --git a/pages/about.tsx b/pages/about.tsx new file mode 100644 index 0000000..5a14d79 --- /dev/null +++ b/pages/about.tsx @@ -0,0 +1,98 @@ +import AppFrame from '../components/AppFrame' +import ModelInfo from '../components/ModelInfo' +import models, {ModelSpec} from '../lib/models' +import styles from './about.module.css' + +export default function IndexPage() { + return ( + +
    +

    About

    + +

    + The COVID Modeling UI was developed to help policy makers explore + hypothetical intervention strategies to reduce the impact of COVID-19. + It provides a common interface and language to run simulations against + multiple models at the same time. +

    + +

    How it works

    +

    + Taking into account existing real-world data, policy makers can run + hypothetical simulations to test different combinations and durations + of intervention strategies. This application runs the simulation + through multiple epidemiology models and presents a single overview + with the projected outcomes. +

    +

    + The UI is independent of the models and architected to support the + addition of new models in the future. It is also designed to support + new intervention strategies that policy makers may consider in the + future, like testing procedures and contact tracing. +

    + +

    Access

    +

    + Because some of the models require large amounts of computing power, + access to the COVID Modeling UI is invitation-only at this time. In + the future, it is likely that pre-computed outcome views will be + visible to the public. +

    + +

    Open Source

    +

    + All code is open source and the relevant repositories are available + under the covid-modeling organization on GitHub. Please record all + feedback, suggestions, and improvements as issues or pull requests on + those repositories. +

    + +

    Models

    +

    + The UI was designed in a collaboration between modeling teams at the + following institutions (in alphabetical order): +

    + + {models.basel && ( + <> +

    Basel University

    + + + )} + + {models['mrc-ide-covid-sim'] && ( + <> +

    Imperial College

    + + + )} + +

    Institute of Disease Modelling

    + + + {models.cosmc && ( + <> +

    Stanford University

    + + + )} + +

    + Many other modeling teams generously provided input and feedback. + Microsoft and GitHub provided software engineering assistance to the + expert modeling teams. +

    +
    +     + ) +} diff --git a/pages/api/callback.ts b/pages/api/callback.ts new file mode 100644 index 0000000..b7d9c6a --- /dev/null +++ b/pages/api/callback.ts @@ -0,0 +1,69 @@ +import {Severity} from '@sentry/node' +import JWT from 'jsonwebtoken' +import {NextApiRequest, NextApiResponse} from 'next' +import 'source-map-support/register' +import {assertEnv} from '../../lib/assertions' +import {isAuthorizedUser} from '../../lib/db' +import {deleteAccessToken, exchangeCode, getUser} from '../../lib/github' +import {catchUnhandledErrors} from '../../lib/handle-error' +import {withDB} from '../../lib/mysql' +import redirect from '../../lib/redirect' +import {initSentry} from '../../lib/sentry' +import {setSessionCookie} from '../../lib/session' + +catchUnhandledErrors() + +const {captureMessage} = initSentry() +const OAUTH_SECRET = assertEnv('OAUTH_SECRET') + +/** + * Handle a GitHub OAuth callback redirect. + */ +export default withDB( + conn => async (req: NextApiRequest, res: NextApiResponse) => { + const code = req.query.code as string + const state = req.query.state as string + + try { + JWT.verify(state, OAUTH_SECRET, {algorithms: ['HS256']}) + } catch (err) { + console.error('OAuth state verification error', err) + captureMessage(`Invalid OAuth state: "${err.message}"`, Severity.Warning) + res.status(400).json({error: 'OAuth state invalid'}) + return + } + + try { + const [client, token] = await exchangeCode(code) + const user = await getUser(client) + + try { + await deleteAccessToken({token}) + } catch (err) { + console.error('Unable to delete OAuth access token') + captureMessage('Unable to delete OAuth access token', Severity.Warning) + } + + if (await isAuthorizedUser(conn, user.login.toLowerCase())) { + setSessionCookie(req, res, {user: {id: user.id, login: user.login}}) + redirect(res, '/simulations') + } else { + redirect(res, '/unauthorized') + } + } catch (err) { + if (err.response) { + console.error( + 'OAuth non-2xx response:', + err.response.status, + err.response.data + ) + } else if (err.request) { + console.error('OAuth request error:', err.message) + } else { + console.error('OAuth error', err) + } + + res.status(500).end('Internal server error') + } + } +) diff --git a/pages/api/login.ts b/pages/api/login.ts new file mode 100644 index 0000000..0e756a1 --- /dev/null +++ b/pages/api/login.ts @@ -0,0 +1,24 @@ +import * as crypto from 'crypto' +import JWT from 'jsonwebtoken' +import * as qs from 'querystring' +import {assertEnv} from '../../lib/assertions' +import dispatch from './util/dispatch' + +const GITHUB_CLIENT_ID = assertEnv('GITHUB_CLIENT_ID') +const OAUTH_SECRET = assertEnv('OAUTH_SECRET') + +export default dispatch('GET', async (req, res) => { + const state = JWT.sign( + {nonce: crypto.randomBytes(32).toString('hex')}, + OAUTH_SECRET, + {algorithm: 'HS256', expiresIn: '10m'} + ) + + const params = qs.encode({ + client_id: GITHUB_CLIENT_ID, + state + }) + + const location = `https://github.com/login/oauth/authorize?${params}` + res.writeHead(307, {location}).end('Temporary redirect') +}) diff --git a/pages/api/logout.ts b/pages/api/logout.ts new file mode 100644 index 0000000..676e37a --- /dev/null +++ b/pages/api/logout.ts @@ -0,0 +1,15 @@ +import {NextApiRequest, NextApiResponse} from 'next' +import 'source-map-support/register' +import {catchUnhandledErrors} from '../../lib/handle-error' +import redirect from '../../lib/redirect' +import {clearSessionCookie} from '../../lib/session' + +catchUnhandledErrors() + +/** + * Log the user out. + */ +export default function logout(req: NextApiRequest, res: NextApiResponse) { + clearSessionCookie(req, res) + redirect(res, '/') +} diff --git a/pages/api/simulations/[id]/case-summary.ts b/pages/api/simulations/[id]/case-summary.ts new file mode 100644 index 0000000..75a7712 --- /dev/null +++ b/pages/api/simulations/[id]/case-summary.ts @@ -0,0 +1,106 @@ +import {DateTime} from 'luxon' +import {last} from '../../../../lib/arrayMath' +import * as db from '../../../../lib/db' +import {withDB} from '../../../../lib/mysql' +import { + ISODate, + ModelOutput, + SeverityMetrics +} from '../../../../types/model-runner' +import {getBlob} from '../../util/blob-storage' +import dispatch from '../../util/dispatch' +import requireSession from '../../util/require-session' + +export type CaseSummary = { + cConf: number + cHosp: number + cDeaths: number + peakDeath: ISODate + peakDailyDeath: number +} + +export default withDB(conn => + requireSession(ssn => + dispatch('GET', async (req, res) => { + const id = parseInt(req.query.id as string) + const sim = await db.getSimulation(conn, ssn.user, {id}) + + if (!sim) { + res.status(404).json({error: 'Not found'}) + return + } + const allResults = await fetchSimulationResults(sim) + + const summarizedResults = allResults.reduce>( + (sum, out) => { + const metrics = out.aggregate.metrics + + // maxIndex finds the last peak value, we want the earliest occurrence (rounded) + const peakDailyDeathIdx = metrics.incDeath.reduce( + ([maxI, maxV], v, i) => + Math.round(v) > maxV ? [i, Math.round(v)] : [maxI, maxV], + [0, 0] + )[0] + + const peakDailyDeath = metrics.incDeath[peakDailyDeathIdx] + const peakDailyDeathTs = out.time.timestamps[peakDailyDeathIdx] + const peakDeath = DateTime.fromISO(out.time.t0).plus({ + days: peakDailyDeathTs + }) + + sum[out.metadata.model.slug] = { + cConf: Math.round(getCumulativeConfirmed(metrics)), + cHosp: Math.round(getCumulativeHospitalized(metrics)), + cDeaths: Math.round(getCumulativeDeaths(metrics)), + peakDeath: peakDeath.toISODate(), + peakDailyDeath: Math.round(peakDailyDeath) + } + + return sum + }, + {} + ) + + res.status(200).json(summarizedResults) + }) + ) +) + +async function fetchSimulationResults( + sim: db.Simulation +): Promise { + // Get all the raw results. + const allRaw = await Promise.all( + sim.model_runs.map(run => + run.results_data ? getBlob(run.results_data) : null + ) + ) + + // Parse all the raw results we found. + return allRaw.filter(isResult).map(r => JSON.parse(r) as ModelOutput) +} + +// Sum of all case types. +function getCumulativeConfirmed(met: SeverityMetrics): number { + return ( + last(met.cumMild) + + last(met.cumILI) + + last(met.cumSARI) + + last(met.cumCritical) + ) +} + +// Sum of all deaths. +function getCumulativeDeaths(met: SeverityMetrics): number { + return met.incDeath.reduce((s, m) => s + m, 0) +} + +// Sum of normal and ICU hospital beds. +function getCumulativeHospitalized(met: SeverityMetrics): number { + return last(met.cumSARI) + last(met.cumCritRecov) + last(met.cumCritical) +} + +function isResult(r: unknown): r is string { + // Type predicate helps the `filter/map` + return r != null +} diff --git a/pages/api/simulations/[id]/download.ts b/pages/api/simulations/[id]/download.ts new file mode 100644 index 0000000..ae6217c --- /dev/null +++ b/pages/api/simulations/[id]/download.ts @@ -0,0 +1,68 @@ +import { + ContainerSASPermissions, + generateBlobSASQueryParameters, + SASProtocol +} from '@azure/storage-blob' +import {DateTime} from 'luxon' +import {getSimulation} from '../../../../lib/db' +import {withDB} from '../../../../lib/mysql' +import { + getContainerClient, + getSharedKeyCredential +} from '../../util/blob-storage' +import dispatch from '../../util/dispatch' +import requireSession from '../../util/require-session' + +export default dispatch( + 'GET', + withDB(conn => + requireSession(ssn => async (req, res) => { + const sim = await getSimulation(conn, ssn.user, { + id: parseInt(req.query.id as string) + }) + + if (!sim) { + res.status(404).json({error: 'Not found'}) + return + } + + const modelRun = sim.model_runs.find( + run => + run.model_slug.toLowerCase() === + (req.query.model as string).toLowerCase() + ) + + if (!modelRun || !modelRun.export_location) { + res.status(404).json({error: 'Not found'}) + return + } + + const url = getSharedBlobURL(modelRun.export_location) + res.writeHead(307, {location: url}).end('Temporary redirect') + }) + ) +) + +function getSharedBlobURL(path: string): string { + const now = new Date() + const expires = DateTime.fromJSDate(now) + .plus({minutes: 10}) + .toJSDate() + + const containerClient = getContainerClient() + + const blob = containerClient.getBlobClient(path) + + const containerSAS = generateBlobSASQueryParameters( + { + containerName: containerClient.containerName, + permissions: ContainerSASPermissions.parse('r'), + startsOn: now, + expiresOn: expires, + protocol: SASProtocol.Https + }, + getSharedKeyCredential() + ).toString() + + return `${blob.url}?${containerSAS}` +} diff --git a/pages/api/simulations/[id]/index.ts b/pages/api/simulations/[id]/index.ts new file mode 100644 index 0000000..316485e --- /dev/null +++ b/pages/api/simulations/[id]/index.ts @@ -0,0 +1,59 @@ +import assert from 'assert' +import {NextApiRequest} from 'next' +import 'source-map-support/register' +import {assertEnv} from '../../../../lib/assertions' +import {updateSimulation} from '../../../../lib/db' +import {catchUnhandledErrors} from '../../../../lib/handle-error' +import {withDB} from '../../../../lib/mysql' +import {SimulationStatus} from '../../../../lib/simulation-types' +import dispatch from '../../util/dispatch' + +catchUnhandledErrors() + +const RUNNER_SHARED_SECRET = assertEnv('RUNNER_SHARED_SECRET', true) + +export default withDB(conn => + dispatch('POST', async (req, res) => { + if (!validateRequest(req)) { + res.status(401).json({error: 'Unauthorized'}) + return + } + + try { + verifyStatus(req.body.status) + + const updated = await updateSimulation( + conn, + req.query.id as string, + req.body.status, + req.body.modelSlug, + req.body.resultsLocation, + req.body.exportLocation, + req.body.workflowRunID + ) + + if (updated) { + res.status(204).end() + } else { + res.status(404).end('Not found') + } + } catch (e) { + res.status(400).json({error: `Could not process message: ${e.message}`}) + } + }) +) + +function verifyStatus(status: SimulationStatus) { + assert( + Object.values(SimulationStatus).includes(status), + new Error(`Invalid status: ${status}`) + ) + return status +} + +function validateRequest(req: NextApiRequest) { + const auth = req.headers.authorization + const authToken = + auth?.startsWith('Bearer ') && auth.slice('Bearer '.length).trim() + return authToken === RUNNER_SHARED_SECRET +} diff --git a/pages/api/simulations/index.ts b/pages/api/simulations/index.ts new file mode 100644 index 0000000..be70b6d --- /dev/null +++ b/pages/api/simulations/index.ts @@ -0,0 +1,137 @@ +import {captureException} from '@sentry/node' +import {ServerlessMysql} from 'serverless-mysql' +import 'source-map-support/register' +import SQL from 'sql-template-strings' +import {assertEnv} from '../../../lib/assertions' +import {toYYYYMMDD} from '../../../lib/dateFunctions' +import { + createSimulation, + getRegionCaseData, + listSimulationSummaries, + updateSimulation +} from '../../../lib/db' +import {createClient, repositoryDispatch} from '../../../lib/github' +import {catchUnhandledErrors} from '../../../lib/handle-error' +import models from '../../../lib/models' +import {withDB} from '../../../lib/mysql' +import { + NewSimulationConfig, + validateSchema +} from '../../../lib/new-simulation-state' +import {Session} from '../../../lib/session' +import {ModelInput, RunStatus} from '../../../types/model-runner' +import dispatch from '../util/dispatch' +import requireSession from '../util/require-session' + +catchUnhandledErrors() + +const CONTROL_REPO_NWO = assertEnv('CONTROL_REPO_NWO', true) +const GITHUB_API_TOKEN = assertEnv('GITHUB_API_TOKEN', true) +const RUNNER_CALLBACK_URL = assertEnv('RUNNER_CALLBACK_URL', true) +const CONTROL_REPO_EVENT_TYPE = assertEnv('CONTROL_REPO_EVENT_TYPE', true) + +export default withDB(conn => + requireSession((session: Session) => + dispatch({ + get: async (_req, res) => { + const summaries = await listSimulationSummaries(conn, session.user.id) + res.status(200).json(summaries) + }, + post: async (req, res) => { + const config: NewSimulationConfig = JSON.parse(req.body) + + const error = validateSchema(config) + if (error) { + res.status(422).json(error) + return + } + + try { + const insertId = await createAndDispatchSimulation( + conn, + session.user, + config + ) + res.status(200).json({id: insertId}) + } catch (err) { + console.error(err) + captureException(err) + res.status(500).json({error: 'Error queueing simulation run'}) + } + } + }) + ) +) + +async function createAndDispatchSimulation( + conn: ServerlessMysql, + user: Session['user'], + config: NewSimulationConfig +): Promise { + await conn.query(SQL`START TRANSACTION`) + + // TODO should we be failing the run of there is no case data? + const {endDate, deaths, confirmed} = await getRegionCaseData( + conn, + config.regionID, + config.subregionID + ) + + const modelInput: Omit = { + region: config.regionID, + subregion: config.subregionID, + parameters: { + r0: typeof config.r0 == 'number' ? config.r0 : null, + calibrationCaseCount: confirmed || 0, + calibrationDeathCount: deaths || 0, + calibrationDate: endDate || toYYYYMMDD(), + interventionPeriods: config.interventionPeriods + } + } + + const {insertId} = await createSimulation(conn, { + region_id: config.regionID, + subregion_id: config.subregionID, + status: RunStatus.Pending, + github_user_id: user.id, + github_user_login: user.login, + label: config.label, + configuration: modelInput + }) + + if (process.env.LOCAL_MODE) { + for (const slug in models) { + await updateSimulation( + conn, + insertId.toString(), + RunStatus.Complete, + slug, + `file://${process.cwd()}/data/result-stub.json`, + '', + undefined + ) + } + } else { + const [owner, name] = CONTROL_REPO_NWO.split('/') + const client = createClient({token: GITHUB_API_TOKEN}) + + try { + await repositoryDispatch(client, owner, name, CONTROL_REPO_EVENT_TYPE, { + id: insertId, + models: Object.entries(models).map(([slug, spec]) => ({ + slug, + imageURL: spec.imageURL + })), + configuration: modelInput, + callbackURL: RUNNER_CALLBACK_URL + }) + } catch (err) { + await conn.query('ROLLBACK') + throw err + } + } + + await conn.query('COMMIT') + + return insertId +} diff --git a/pages/api/types/async-next-api-handler.ts b/pages/api/types/async-next-api-handler.ts new file mode 100644 index 0000000..b89e98f --- /dev/null +++ b/pages/api/types/async-next-api-handler.ts @@ -0,0 +1,5 @@ +import {NextApiHandler} from 'next' + +export type AsyncNextApiHandler = ( + ...args: Parameters> +) => Promise>> diff --git a/pages/api/user/accept-disclaimer.ts b/pages/api/user/accept-disclaimer.ts new file mode 100644 index 0000000..d1f4a05 --- /dev/null +++ b/pages/api/user/accept-disclaimer.ts @@ -0,0 +1,17 @@ +import {updateUserConfig} from '../../../lib/db' +import {withDB} from '../../../lib/mysql' +import dispatch from '../util/dispatch' +import requireSession from '../util/require-session' + +export default withDB(conn => + requireSession(session => + dispatch('POST', async (req, res) => { + await updateUserConfig(conn, session.user.login, config => ({ + ...config, + hasAcceptedDisclaimer: true + })) + + res.json({ok: true}) + }) + ) +) diff --git a/pages/api/util/blob-storage.ts b/pages/api/util/blob-storage.ts new file mode 100644 index 0000000..9e0c0e0 --- /dev/null +++ b/pages/api/util/blob-storage.ts @@ -0,0 +1,41 @@ +import { + BlobServiceClient, + StorageSharedKeyCredential +} from '@azure/storage-blob' +import {assertEnv} from '../../../lib/assertions' + +const BLOB_STORAGE_ACCOUNT = assertEnv('BLOB_STORAGE_ACCOUNT', true) +const BLOB_STORAGE_KEY = assertEnv('BLOB_STORAGE_KEY', true) +const BLOB_STORAGE_CONTAINER = assertEnv('BLOB_STORAGE_CONTAINER', true) + +export function getSharedKeyCredential() { + return new StorageSharedKeyCredential(BLOB_STORAGE_ACCOUNT, BLOB_STORAGE_KEY) +} + +export function getContainerClient() { + const client = new BlobServiceClient( + `https://${BLOB_STORAGE_ACCOUNT}.blob.core.windows.net`, + getSharedKeyCredential() + ) + + return client.getContainerClient(BLOB_STORAGE_CONTAINER) +} + +export async function getBlob(path: string): Promise { + if (process.env.LOCAL_MODE) { + return JSON.stringify(require('../../../data/result-stub.json')) + } + + const blob = getContainerClient().getBlobClient(path) + + try { + const buffer = await blob.downloadToBuffer() + return buffer.toString('utf-8') + } catch (err) { + if (err.statusCode === 404) { + return null + } + + throw err + } +} diff --git a/pages/api/util/dispatch.ts b/pages/api/util/dispatch.ts new file mode 100644 index 0000000..7c1611c --- /dev/null +++ b/pages/api/util/dispatch.ts @@ -0,0 +1,57 @@ +import {NextApiRequest, NextApiResponse} from 'next' +import {AsyncNextApiHandler} from '../types/async-next-api-handler' + +export default function dispatch( + method: string, + handler: AsyncNextApiHandler +): AsyncNextApiHandler + +export default function dispatch( + handlers: Record +): AsyncNextApiHandler + +export default function dispatch( + methodOrHandlers: string | Record, + handler?: AsyncNextApiHandler +) { + return (req: NextApiRequest, res: NextApiResponse) => { + if (typeof methodOrHandlers === 'string') { + return dispatchMethod(methodOrHandlers, handler!)(req, res) + } else { + return dispatchMap(methodOrHandlers)(req, res) + } + } +} + +function dispatchMethod( + method: string, + handler: AsyncNextApiHandler +): AsyncNextApiHandler { + return async (req: NextApiRequest, res: NextApiResponse) => { + if (method.toLowerCase() !== req.method!.toLowerCase()) { + notFound(res) + return + } + + return handler(req, res) + } +} + +function dispatchMap( + handlers: Record +): AsyncNextApiHandler { + return async (req: NextApiRequest, res: NextApiResponse) => { + const handler = handlers[req.method!.toLowerCase()] + + if (!handler) { + notFound(res) + return + } + + return handler(req, res) + } +} + +function notFound(res: NextApiResponse) { + res.status(404).end('Not found') +} diff --git a/pages/api/util/require-session.ts b/pages/api/util/require-session.ts new file mode 100644 index 0000000..791b1c5 --- /dev/null +++ b/pages/api/util/require-session.ts @@ -0,0 +1,16 @@ +import {getSessionCookie, Session} from '../../../lib/session' +import {AsyncNextApiHandler} from '../types/async-next-api-handler' + +export default function requireSession( + cb: (session: Session) => AsyncNextApiHandler +): AsyncNextApiHandler { + return async (req, res) => { + const session = getSessionCookie(req, res) + + if (!session) { + res.status(401).end('Unauthorized') + } else { + return cb(session)(req, res) + } + } +} diff --git a/pages/index.module.css b/pages/index.module.css new file mode 100644 index 0000000..f57144a --- /dev/null +++ b/pages/index.module.css @@ -0,0 +1,17 @@ +.IndexContent { + @apply flex items-center justify-center; + @apply flex-1; + height: 100%; +} + +.LoginLink { + @apply flex items-center justify-center; + @apply bg-black; + @apply px-4 py-3; + @apply rounded; + @apply text-sm text-white; +} + +.LoginLink svg { + @apply mr-4; +} diff --git a/pages/index.tsx b/pages/index.tsx new file mode 100644 index 0000000..bca08d8 --- /dev/null +++ b/pages/index.tsx @@ -0,0 +1,20 @@ +import AppFrame from '../components/AppFrame' +import Button from '../components/Button' +import handleError from '../lib/handle-error' +import {refuteSession} from '../lib/session' +import GitHub from '../svg/GitHub.svg' +import styles from './index.module.css' + +export default function IndexPage() { + return ( + + + + ) +} + +export const getServerSideProps = handleError(refuteSession()) diff --git a/pages/logout.tsx b/pages/logout.tsx new file mode 100644 index 0000000..561960d --- /dev/null +++ b/pages/logout.tsx @@ -0,0 +1,11 @@ +import {GetServerSideProps} from 'next' +import handleError from '../lib/handle-error' +import redirect from '../lib/redirect' + +/* eslint-disable-next-line */ +export default function LogoutPage() {} + +export const getServerSideProps: GetServerSideProps = handleError(async ctx => { + redirect(ctx.res, '/api/logout') + return {props: {}} +}) diff --git a/pages/meta/_boom.tsx b/pages/meta/_boom.tsx new file mode 100644 index 0000000..0221da7 --- /dev/null +++ b/pages/meta/_boom.tsx @@ -0,0 +1,100 @@ +import {GetServerSideProps} from 'next' +import {useContext, useState} from 'react' +import Button from '../../components/Button' +import handleError from '../../lib/handle-error' +import {ensureSession} from '../../lib/session' +import {SentryContext} from '../_app' + +const DEFAULT_MESSAGE = 'Test Error' + +export default function MetaBoomPage() { + const {captureException} = useContext(SentryContext) + const [message, setMessage] = useState(DEFAULT_MESSAGE) + const [type, setType] = useState('catch-and-report') + const [rethrow, setRethrow] = useState(false) + + return ( +
    { + console.log('Testing error with', type) + + e.preventDefault() + + if (type === 'catch-and-report') { + try { + throw new Error(message) + } catch (err) { + captureException(err) + + if (rethrow) { + throw err + } + } + } else { + throw new Error(message) + } + }} + > +

    Test Error

    + + setMessage(e.target.value)} + autoFocus + className="block w-full p-4 rounded mb-4 border outline-none focus:shadow-outline" + /> +
    + setType('catch-and-report')} + /> + + {type === 'catch-and-report' && ( + <> + setRethrow(!rethrow)} + id="rethrow" + /> + + + )} + setType('throw')} + /> + +
    + +
    + +
    + ) +} + +export const getServerSideProps: GetServerSideProps = ensureSession( + handleError(async ctx => { + if (ctx.query['throw-ssp']) { + throw new Error(`${ctx.query.message || DEFAULT_MESSAGE}`) + } + + return {props: {}} + }) +) diff --git a/pages/simulations/[id].tsx b/pages/simulations/[id].tsx new file mode 100644 index 0000000..1756b50 --- /dev/null +++ b/pages/simulations/[id].tsx @@ -0,0 +1,322 @@ +import pick from 'lodash/pick' +import {DateTime} from 'luxon' +import {GetServerSideProps} from 'next' +import NextError from 'next/error' +import Link from 'next/link' +import {useRouter} from 'next/router' +import AppFrame from '../../components/AppFrame' +import CaseSummary from '../../components/CaseSummary' +import ChartWrapper from '../../components/ChartWrapper' +import Disclaimer from '../../components/Disclaimer' +import IncompleteSimulation from '../../components/IncompleteSimulation' +import ModelInfo from '../../components/ModelInfo' +import ModelSelect from '../../components/ModelSelect' +import SimulationInputsTable from '../../components/SimulationInputsTable' +import SimulationList from '../../components/SimulationList' +import btnStyles from '../../components/styles/button.module.css' +import { + getFatalityData, + getSimulation, + getUserConfig, + listSimulationSummaries, + ModelRun, + Simulation, + SimulationSummary +} from '../../lib/db' +import handleError from '../../lib/handle-error' +import * as logging from '../../lib/logging' +import models from '../../lib/models' +import {withDB} from '../../lib/mysql' +import flagAndName from '../../lib/regionEmoji' +import {ensureSession} from '../../lib/session' +import Download from '../../svg/Download.svg' +import {CaseData} from '../../types/case-data' +import {ModelOutput, RunStatus} from '../../types/model-runner' +import {getBlob} from '../api/util/blob-storage' +import styles from './simulation.module.css' + +type Props = { + hasAcceptedDisclaimer: boolean + simulation: Simulation | null + summaries: SimulationSummary[] + result: ModelOutput | null + caseData: CaseData | null + modelRun: ModelRun | null + modelSlug: string + showDebug: boolean +} + +export default function AppFrameWrapper(props: Props) { + return ( + + + + ) +} + +function SimulationPage(props: Props) { + const router = useRouter() + + if (!props.simulation || !props.modelRun) { + return + } + + logProps(props) + + const modelSlug = props.modelRun.model_slug + + const changeModel = (modelSlug: string) => { + router.push('/simulations/[id]', { + pathname: `/simulations/${props.simulation!.id}`, + query: {model: modelSlug} + }) + } + + return ( +
    +
    + + +
    + {!props.hasAcceptedDisclaimer ? ( + + ) : ( +
    +
    +
    +
    + {flagAndName( + props.simulation.region_id, + props.simulation.region_name + )}{' '} + {props.simulation.subregion_name + ? `/ ${props.simulation.subregion_name}` + : null}{' '} + · Created{' '} + {DateTime.fromISO(props.simulation.created_at).toRelative()} +
    + +

    + {props.simulation.label || 'Untitled Simulation'} +

    +
    + + {props.modelRun.export_location ? ( + + ) : null} +
    + + {props.modelRun.status !== RunStatus.Complete ? ( +
    + r.model_slug + )} + onChange={changeModel} + /> +
    + ) : null} + + {props.modelRun.status === RunStatus.Pending ? ( + + ) : props.modelRun.status === RunStatus.InProgress ? ( + + ) : props.modelRun.status === RunStatus.Failed ? ( + + ) : !props.result || !props.caseData ? ( + + ) : ( + <> + + + + + )} +
    + )} + + + +

    Model information

    + +
    + {Object.entries(models).map(([slug, modelSpec]) => ( + + ))} +
    +
    +
    +
    + ) +} + +export const getServerSideProps: GetServerSideProps = handleError( + withDB(conn => + ensureSession(async (ctx, session) => { + const id = Number(ctx.params?.id) + const modelSlug = Array.isArray(ctx.query.model) + ? ctx.query.model[0] || 'mrc-ide-covid-sim' + : ctx.query.model || 'mrc-ide-covid-sim' + + const showDebug = Boolean(ctx.query.debug) + + if (id == null || isNaN(id)) { + const props: Props = { + hasAcceptedDisclaimer: false, + simulation: null, + summaries: [], + result: null, + caseData: null, + modelRun: null, + modelSlug, + showDebug + } + + return {props} + } + + const simulation = await getSimulation(conn, session.user, {id}) + const modelRun = simulation?.model_runs.find( + run => run.model_slug === modelSlug + ) + const summaries = await listSimulationSummaries(conn, session.user.id) + + if (!simulation || !modelRun) { + const props: Props = { + hasAcceptedDisclaimer: false, + simulation: null, + summaries: [], + result: null, + caseData: null, + modelRun: null, + modelSlug, + showDebug + } + + return {props} + } + + let result: ModelOutput | null = null + let caseData: CaseData | null = null + if (modelRun.status === RunStatus.Complete) { + const resultsData = simulation.model_runs.find( + run => run.model_slug === modelSlug + )?.results_data + const rawResult = resultsData ? await getBlob(resultsData) : null + + if (rawResult) { + result = JSON.parse(rawResult) as ModelOutput + + caseData = await getFatalityData( + conn, + simulation.region_id, + simulation.subregion_id, + result.time.t0, + result.time.extent + ) + } + } + + if (!Object.keys(models).includes(modelSlug)) { + // invalid model + ctx.res.writeHead(404).end() + } + + const userConf = await getUserConfig(conn, session.user.login) + + const props: Props = { + hasAcceptedDisclaimer: Boolean(userConf.hasAcceptedDisclaimer), + simulation, + summaries, + result, + caseData, + modelRun, + modelSlug, + showDebug + } + + return {props} + }) + ) +) + +function logProps(props: Props) { + if (!process.browser) return + if (!props.showDebug) return + + logging.group(`Simulation Results Data (${props.modelSlug})`, () => { + logging.logValue( + 'Simulation Metadata', + pick(props.simulation, [ + 'id', + 'status', + 'region_name', + 'region_id', + 'subregion_name', + 'subregion_id', + 'github_user_id', + 'github_user_login', + 'created_at', + 'updated_at' + ]) + ) + logging.logValue( + 'Configuration Parameters', + props.simulation?.configuration.parameters + ) + logging.logValue('Models Runs', props.simulation?.model_runs) + logging.logValue('Result Metadata', props.result?.metadata) + + logging.group('Raw Props', () => console.log(props)) + }) +} diff --git a/pages/simulations/index.module.css b/pages/simulations/index.module.css new file mode 100644 index 0000000..be6a005 --- /dev/null +++ b/pages/simulations/index.module.css @@ -0,0 +1,9 @@ +.wrapper { + @apply flex flex-col; + @apply h-full; +} + +.container { + @apply flex flex-col items-center justify-center; + @apply flex-1; +} diff --git a/pages/simulations/index.tsx b/pages/simulations/index.tsx new file mode 100644 index 0000000..c859bd5 --- /dev/null +++ b/pages/simulations/index.tsx @@ -0,0 +1,62 @@ +import {GetServerSideProps} from 'next' +import Link from 'next/link' +import {useRouter} from 'next/router' +import AppFrame from '../../components/AppFrame' +import button from '../../components/styles/button.module.css' +import * as db from '../../lib/db' +import {SimulationSummary} from '../../lib/db' +import handleError from '../../lib/handle-error' +import {withDB} from '../../lib/mysql' +import {ensureSession} from '../../lib/session' +import styles from './index.module.css' + +type Props = { + lastSimulation: SimulationSummary | null +} + +export default function SimulationsIndexPage(props: Props) { + const router = useRouter() + + if (props.lastSimulation && process.browser) { + router.push('/simulations/[id]', `/simulations/${props.lastSimulation.id}`) + return null + } + + return ( + +
    +
    +

    No simulations created yet

    + +

    + Get started by creating a new simulation for this region. After your + first simulation is created, the results will be visible here. +

    + + + + + Create new simulation + + +
    +
    +     + ) +} + +export const getServerSideProps: GetServerSideProps = handleError( + withDB(conn => + ensureSession(async (ctx, session) => { + const lastSimulation = + ( + await db.listSimulationSummaries(conn, session.user.id, {limit: 1}) + )[0] || null + + return { + props: { + lastSimulation + } + } + }) + ) +) diff --git a/pages/simulations/new.module.css b/pages/simulations/new.module.css new file mode 100644 index 0000000..66f121a --- /dev/null +++ b/pages/simulations/new.module.css @@ -0,0 +1,77 @@ +.NewSimulationPage { + @apply mx-auto; + margin-top: 49px; + max-width: 595px; +} + +.NewSimulationPage h1 { + @apply mt-2 mb-14; + @apply font-bold; + @apply text-2xl; +} + +.ApplicationConfig { + @apply flex items-start; + @apply mb-8; + @apply text-sm; +} + +.ApplicationConfigContent { + @apply flex-1; + @apply ml-3; +} + +.ApplicationConfigContent p { + @apply text-light-gray; +} + +.ApplicationConfig h3 { + @apply font-semibold; +} + +.ApplicationConfigParams { + @apply flex; +} + +.NewSubmit { + width: 100%; +} + +.NewSubmit>span { + width: 100%; +} + +.NewConfigurationTitle { + @apply my-2; + @apply mx-1; +} + +.NewConfigurationTitle h3 { + @apply font-semibold; + @apply text-base; + @apply mt-3; +} + +.NewConfigurationTitle p { + color: #52555F; +} + +.CalibrationControl { + @apply border-solid; + @apply border; + @apply p-3; + @apply mb-2; + display: inline-block; + width: 100%; +} + +.CalibrationControl input, +.CalibrationControl>div { + width: 100%; +} + +.Error.CalibrationControl { + @apply border-solid; + @apply border; + border-color: red; +} diff --git a/pages/simulations/new.tsx b/pages/simulations/new.tsx new file mode 100644 index 0000000..827c21b --- /dev/null +++ b/pages/simulations/new.tsx @@ -0,0 +1,43 @@ +import AppFrame from '../../components/AppFrame' +import NewSimulationForm from '../../components/simulation-form/NewSimulationForm' +import * as db from '../../lib/db' +import handleError from '../../lib/handle-error' +import {withDB} from '../../lib/mysql' +import {ensureSession} from '../../lib/session' +import {InterventionMap} from '../../lib/simulation-types' +import {RegionMap} from '../../types/regions' + +interface Props { + regions: RegionMap + interventions: InterventionMap +} + +export default function NewSimulationPage(props: Props) { + return ( + + + + ) +} + +let interventions: InterventionMap + +export const getServerSideProps = handleError( + withDB(conn => + ensureSession(async () => { + const regions = require('../../data/regions.json') + + // Cache intervention data for the life of the server process + if (!interventions) { + interventions = await db.getInterventionData(conn) + } + + return { + props: { + regions, + interventions + } + } + }) + ) +) diff --git a/pages/simulations/simulation.module.css b/pages/simulations/simulation.module.css new file mode 100644 index 0000000..af5cd18 --- /dev/null +++ b/pages/simulations/simulation.module.css @@ -0,0 +1,65 @@ +.SimulationPage { + @apply mx-auto; + @apply px-8 pt-4 pb-8; + @apply h-full; +} + +.SimulationBody { + @apply flex flex-wrap; + @apply items-stretch; +} + +.SimulationLeft { + @apply mr-8; + @apply flex-none; + @apply w-80; +} + +.SimulationRight { + @apply flex-1; +} + +.Assumptions { + @apply mt-16; +} + +.AssumptionsLinks { + @apply mt-6; +} + +.AssumptionsLinks a { + @apply mr-4 py-3 px-4; + @apply text-sm; + @apply border rounded; +} + +.regionHeading { + @apply text-sm; + @apply text-gray-600; +} + +.modelInfoWrapper { + @apply grid-cols-1; + + display: grid; + grid-column-gap: 1.5rem; + grid-row-gap: 1.5rem; +} + +@screen sm { + .SimulationRight { + @apply min-w-full; + } +} + +@screen md { + .modelInfoWrapper { + @apply grid-cols-2; + } +} + +@screen lg { + .SimulationRight { + @apply min-w-0; + } +} diff --git a/pages/unauthorized.tsx b/pages/unauthorized.tsx new file mode 100644 index 0000000..cb31157 --- /dev/null +++ b/pages/unauthorized.tsx @@ -0,0 +1,14 @@ +import Error from 'next/error' +import handleError from '../lib/handle-error' +import {refuteSession} from '../lib/session' + +export default function RequestAccessPage() { + return ( + + ) +} + +export const getServerSideProps = handleError(refuteSession()) diff --git a/postcss.config.js b/postcss.config.js new file mode 100644 index 0000000..3427537 --- /dev/null +++ b/postcss.config.js @@ -0,0 +1,16 @@ +/** @type {(string | [string, object])[]} */ +const plugins = ['postcss-import', 'tailwindcss', 'autoprefixer'] + +if (process.env.NODE_ENV === 'production') { + plugins.push([ + '@fullhuman/postcss-purgecss', + { + content: ['**/*.tsx', '**/*.module.css', 'css/app.css'], + whitelistPatterns: [/^ReactVirtualized/, /bg-*/, /text-severity*/] + } + ]) +} + +module.exports = { + plugins +} diff --git a/public/images/google.png b/public/images/google.png new file mode 100644 index 0000000000000000000000000000000000000000..1bb121c77a675c59f6250b4b7245a5d8012079a3 GIT binary patch literal 1236 zcmV;_1S|WAP)Ko9M8RK*|v8dlo?#_H?zH{!( zH#55kae|79RBr~X1H@{QVih2z%niZ-_ji&7k2!wmJ{^xP#tInQSdbC$TVDdA=Q%hN z;s%`|pm!Z@u8&~81$ZippCf=b5pglhAA>})#?kH?f_Mu!Us{@Fv(rIN{va$2LPW6B z(cbe;%mOY}mE5jr(8gbv!vcZ}aH~QVWVX64hxd!{hOf$*BQt`p|p@cUk zHS7Bbv@8z65ni4a3&Ec}hm+C*i%?P_kg-b^nI+Hd{LO8qHC@1HW$AWy?G}iZ7@NMr6oT(nNZY2#H1;TBylIt)$;HfBCA_es5gCYe=fZdL^o+chZ5Caz~3i1?- zx-Xst<6&>9OglYFK4%QzXu6`VL}b*sib>`A+_clU{YvS05&Ho zxuG9yRn{Y6p5CxJFG705Ac%~BLF#Mh(>!}1fnZO;h8Z24+}hD3wFt00n#2v^MJ zhP9NO?MIz!4?OZqS5ysxHn#AUXffGkGy(ST63;8)WX@#lldyI{ve8H`J-z79_oep2g%n*c)k zV-YztW)FamKi#;_b0Kl-3hG!?|-v7FJ@ z3gWLoL}Rt&0nn1pg5_#HpiCL1pjOebJN>We(Po1R57j;^koGdIzyd)8b3C?@z4!n8 zimf-iKjKt7KdxJ$s`5Ao a.date - b.date) + .map(row => { + const regionID = 'US' + const subregionID = `US-${row.state}` + + // Date is an integer with digits YYYYMMDD + const dateString = row.date.toString() + const date = new Date( + dateString.slice(0, 4), + parseInt(dateString.slice(4, 6), 10) - 1, + dateString.slice(6) + ) + const dateSQL = DateTime.fromJSDate(date).toISODate() + + // Fill in null values with the last non-null value or zero + const current = + metricsByState[row.state] || (metricsByState[row.state] = {}) + current.confirmed = row.positive || current.confirmed || 0 + current.recovered = row.recovered || current.recovered || 0 + current.deaths = row.death || current.deaths || 0 + + return [ + regionID, + subregionID, + dateSQL, + current.confirmed, + current.recovered, + current.deaths + ] + }) + + // Parse the UK case data + const ukCaseRecordsByDate = {} + for (const [metric, csv] of [ + ['confirmed', globalConfirmedCSV], + ['recovered', globalRecoveredCSV], + ['deaths', globalDeathsCSV] + ]) { + // Parse the CSV and find the row that corresponds to the entire UK + const data = parseCSV(csv) + const ukRow = data.findIndex( + row => row[0] === '' && row[1] === 'United Kingdom' + ) + if (ukRow === -1) { + throw new Error(`No United Kingdom row in ${metric} dataset`) + } + + // Combine the data from the per-metric CSVs by building up an object + // whose keys are dates, and whose values contain all the metrics. + const METADATA_COLS = 4 + for (let i = METADATA_COLS; i < data[0].length; i++) { + const dateString = data[0][i] + let record = ukCaseRecordsByDate[dateString] + if (!record) { + // Date is a string with format MM/DD/YY + const [month, day, year] = dateString.split('/') + const date = new Date('20' + year, parseInt(month, 10) - 1, day) + record = ukCaseRecordsByDate[dateString] = { + date: DateTime.fromJSDate(date).toISODate() + } + } + record[metric] = parseFloat(data[ukRow][i], 10) + } + } + const ukCaseRecords = Object.values(ukCaseRecordsByDate).map(r => { + return ['GB', null, r.date, r.confirmed, r.recovered, r.deaths] + }) + + const caseRecords = usCaseRecords.concat(ukCaseRecords) + + // Parse the US intervention data + const usInterventionRecords = [] + for (const row of d3.csvParse(usInterventionsCSV)) { + if (row.StatePolicy && row.StatePostal && row.DateEnacted) { + const regionId = 'US' + const subregionId = `US-${row.StatePostal}` + const policy = row.StatePolicy + const notes = row.PolicyCodingNotes + const source = row.PolicySource || null + const issueDate = row.DateIssued || null + const startDate = row.DateEnacted + const easeDate = row.DateEased || null + const expirationDate = row.DateExpiry || null + const endDate = row.DateEnded || null + usInterventionRecords.push([ + regionId, + subregionId, + policy, + notes, + source, + issueDate, + startDate, + easeDate, + expirationDate, + endDate + ]) + } + } + + if (cacheDir) { + fs.writeFileSync( + path.join(cacheDir, 'case-data.json'), + JSON.stringify(caseRecords, null, 2), + 'utf8' + ) + + fs.writeFileSync( + path.join(cacheDir, 'intervention-data.json'), + JSON.stringify(usInterventionRecords, null, 2), + 'utf8' + ) + } + + try { + await db.query('START TRANSACTION') + + // Populate the case_data table + console.log(`Saving ${caseRecords.length} records to case_data table...`) + await db.query('CREATE TABLE case_data_import LIKE case_data') + await db.query( + ` + INSERT INTO case_data_import + (region_id, subregion_id, date, confirmed, recovered, deaths) + VALUES + ? + `, + [caseRecords] + ) + await db.query( + 'RENAME TABLE case_data TO case_data_old, case_data_import TO case_data' + ) + + // Populate the intervention_data table + await db.query( + 'CREATE TABLE intervention_data_import LIKE intervention_data' + ) + await db.query( + ` + INSERT INTO intervention_data_import + ( + region_id, subregion_id, policy, notes, source, + issue_date, start_date, ease_date, expiration_date, end_date + ) + VALUES + ? + `, + [usInterventionRecords] + ) + await db.query( + 'RENAME TABLE intervention_data TO intervention_data_old, intervention_data_import TO intervention_data' + ) + + await db.query('COMMIT') + } finally { + await db.query('DROP TABLE IF EXISTS case_data_old') + await db.query('DROP TABLE IF EXISTS case_data_import') + await db.query('DROP TABLE IF EXISTS intervention_data_old') + await db.query('DROP TABLE IF EXISTS intervention_data_import') + } +} + +async function fetchCached(url, cacheDir) { + const cacheFilename = path.basename(url) + const cachePath = cacheDir && path.join(cacheDir, cacheFilename) + + if (cachePath && fs.existsSync(cachePath)) { + console.log(`Using existing download ${cachePath}...`) + return fs.readFileSync(cachePath, 'utf8') + } else { + console.log(`Downloading from ${url}...`) + let result = '' + await new Promise((resolve, reject) => { + fetch(url) + function fetch(url) { + https.get(url, res => { + // Follow path redirects + if (res.statusCode === 301 || res.statusCode === 302) { + const oldURL = URL.parse(url) + const locationURL = URL.parse(res.headers.location) + oldURL.path = locationURL.path + oldURL.pathname = locationURL.pathname + oldURL.href = null + const redirectURL = URL.format(oldURL) + console.log(`Redirected\n from ${url}\n to ${redirectURL}...`) + fetch(redirectURL) + } else { + res.on('data', chunk => (result += chunk)) + res.on('end', resolve) + res.on('error', reject) + } + }) + } + }) + if (cachePath) { + console.log(`Saving download to ${cachePath}...`) + fs.writeFileSync(cachePath, result, 'utf8') + } + return result + } +} + +function parseCSV(data) { + return data.split('\n').map(line => line.split(',')) +} + +main() + .then(() => { + process.exit(0) + }) + .catch(error => { + console.error(error) + process.exit(1) + }) diff --git a/script/server b/script/server new file mode 100755 index 0000000..ea5a8c8 --- /dev/null +++ b/script/server @@ -0,0 +1,5 @@ +#!/bin/bash + +set -e + +docker-compose up diff --git a/script/setup b/script/setup new file mode 100755 index 0000000..75fe2f9 --- /dev/null +++ b/script/setup @@ -0,0 +1,95 @@ +#!/usr/bin/env node + +const crypto = require('crypto') +const fs = require('fs') +const path = require('path') +const prompts = require('prompts') +const yaml = require('js-yaml') +const envfile = require('envfile') +const currentEnv = readEnv() + +/** + * @typedef {Object} spec + * @property {string} description + * @property {boolean | undefined} local_mode + * @property {boolean | undefined} secret + * @property {string | undefined} default + * @property {generate | undefined} generate + */ + +/** + * @typedef {Object} generate + * @property {boolean | undefined} secret + */ + +/** + * @type {Record} + */ +const envSpec = yaml.load( + fs.readFileSync(path.join(__dirname, '../env.yml')).toString() +) + +async function main() { + const {LOCAL_MODE} = await prompts({ + type: 'confirm', + name: 'LOCAL_MODE', + message: 'Run in local mode, where remote data is stubbed?' + }) + + const result = LOCAL_MODE ? {...currentEnv, LOCAL_MODE: true} : currentEnv + + for (const key in envSpec) { + const spec = envSpec[key] + + if (key === 'LOCAL_MODE') { + continue + } + + if (LOCAL_MODE && spec.local_mode === false) { + continue + } + + let defaultValue = currentEnv[key] || spec.default + + if (!defaultValue && spec.generate && spec.generate.secret) { + defaultValue = crypto.randomBytes(32).toString('hex') + } + + const response = await prompts({ + type: 'text', + name: key, + message: spec.description, + initial: defaultValue, + style: spec.secret ? 'password' : 'default' + }) + + result[key] = response[key] + } + + const finalEnv = Object.entries(result).reduce( + (dotenv, [key, value]) => dotenv + `${key}=${value}\n`, + `` + ) + + fs.writeFileSync(path.join(__dirname, '../.env'), finalEnv) +} + +main() + .then(() => { + process.exit(0) + }) + .catch(err => { + console.error(err) + process.exit(1) + }) + +function readEnv() { + let env + try { + env = fs.readFileSync(path.join(__dirname, '../.env')).toString() + } catch (err) { + return {} + } + + return envfile.parseSync(env) +} diff --git a/script/staging-alias b/script/staging-alias new file mode 100755 index 0000000..df55117 --- /dev/null +++ b/script/staging-alias @@ -0,0 +1,5 @@ +#!/bin/bash + +set -e + +npx now alias $1 staging.covid-modeling.org diff --git a/svg/Check.svg b/svg/Check.svg new file mode 100644 index 0000000..0bf0edd --- /dev/null +++ b/svg/Check.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/Chevron.svg b/svg/Chevron.svg new file mode 100644 index 0000000..e5eb8e7 --- /dev/null +++ b/svg/Chevron.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/CircleCheck.svg b/svg/CircleCheck.svg new file mode 100644 index 0000000..0625651 --- /dev/null +++ b/svg/CircleCheck.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/Clock.svg b/svg/Clock.svg new file mode 100644 index 0000000..d586111 --- /dev/null +++ b/svg/Clock.svg @@ -0,0 +1,4 @@ + + + + diff --git a/svg/Code.svg b/svg/Code.svg new file mode 100644 index 0000000..5b668ff --- /dev/null +++ b/svg/Code.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/Cross.svg b/svg/Cross.svg new file mode 100644 index 0000000..045dd02 --- /dev/null +++ b/svg/Cross.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/Descartes.svg b/svg/Descartes.svg new file mode 100644 index 0000000..b992850 --- /dev/null +++ b/svg/Descartes.svg @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/svg/Dot.svg b/svg/Dot.svg new file mode 100644 index 0000000..e0aaac1 --- /dev/null +++ b/svg/Dot.svg @@ -0,0 +1 @@ + diff --git a/svg/Download.svg b/svg/Download.svg new file mode 100644 index 0000000..250a1d0 --- /dev/null +++ b/svg/Download.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/Failure.svg b/svg/Failure.svg new file mode 100644 index 0000000..8dc8806 --- /dev/null +++ b/svg/Failure.svg @@ -0,0 +1,4 @@ + + + + diff --git a/svg/Fork.svg b/svg/Fork.svg new file mode 100644 index 0000000..b043b94 --- /dev/null +++ b/svg/Fork.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/GitHub.svg b/svg/GitHub.svg new file mode 100644 index 0000000..b2fd5be --- /dev/null +++ b/svg/GitHub.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/Info.svg b/svg/Info.svg new file mode 100644 index 0000000..6c5936c --- /dev/null +++ b/svg/Info.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/Link.svg b/svg/Link.svg new file mode 100644 index 0000000..c9d3510 --- /dev/null +++ b/svg/Link.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/Plus.svg b/svg/Plus.svg new file mode 100644 index 0000000..1a3fa6c --- /dev/null +++ b/svg/Plus.svg @@ -0,0 +1,4 @@ + + + + diff --git a/svg/Pushpin.svg b/svg/Pushpin.svg new file mode 100644 index 0000000..01fafa3 --- /dev/null +++ b/svg/Pushpin.svg @@ -0,0 +1,7 @@ + + + diff --git a/svg/Share.svg b/svg/Share.svg new file mode 100644 index 0000000..646e53b --- /dev/null +++ b/svg/Share.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/SocialDistancingGraphic.svg b/svg/SocialDistancingGraphic.svg new file mode 100644 index 0000000..c07a008 --- /dev/null +++ b/svg/SocialDistancingGraphic.svg @@ -0,0 +1,17 @@ + + + + + + + + + + + + + + + + + diff --git a/svg/StatusSpinner.svg b/svg/StatusSpinner.svg new file mode 100644 index 0000000..09ad440 --- /dev/null +++ b/svg/StatusSpinner.svg @@ -0,0 +1,4 @@ + + + + diff --git a/svg/Success.svg b/svg/Success.svg new file mode 100644 index 0000000..d87f760 --- /dev/null +++ b/svg/Success.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/Trash.svg b/svg/Trash.svg new file mode 100644 index 0000000..6e5af27 --- /dev/null +++ b/svg/Trash.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/Unacast.svg b/svg/Unacast.svg new file mode 100644 index 0000000..474ad62 --- /dev/null +++ b/svg/Unacast.svg @@ -0,0 +1,22 @@ + + + + + + + diff --git a/svg/Warn.svg b/svg/Warn.svg new file mode 100644 index 0000000..6956b20 --- /dev/null +++ b/svg/Warn.svg @@ -0,0 +1,3 @@ + + + diff --git a/svg/Zip.svg b/svg/Zip.svg new file mode 100644 index 0000000..13c81d5 --- /dev/null +++ b/svg/Zip.svg @@ -0,0 +1,3 @@ + + + diff --git a/tailwind.config.js b/tailwind.config.js new file mode 100644 index 0000000..d2f4bd1 --- /dev/null +++ b/tailwind.config.js @@ -0,0 +1,102 @@ +module.exports = { + theme: { + extend: { + screens: { + '2xl': '1408px' + }, + colors: { + black: '#050505', + 'light-blue': '#f1f8ff', + gray: { + default: '#f7f7f9', + light: '#9194A1', + lightest: '#EFF0F5', + '100': '#f5f5f5', + '200': '#eeeeee', + '300': '#e0e0e0', + '400': '#bdbdbd', + '500': '#9e9e9e', + '600': '#757575', + '700': '#616161', + '800': '#424242', + '900': '#212121' + }, + 'light-gray': '#525560', + purple: '#6F42C1', + red: '#D73A49', + green: '#28A745', + orange: { + default: '#f66a0a', + '100': '#fff8f2', + '200': '#eee6d5', + '300': '#d15704', + '400': '#a04100' + }, + blue: { + default: '#0366D6', + light: '#d9e8f9' + }, + pink: '#D03592', + severity: { + mild: '#fffdef', + moderate: '#ffebda', + aggressive: '#ffdce0' + }, + severitytext: { + mild: '#735c0f;', + moderate: '#a04100', + aggressive: '#86181d' + }, + severityhover: { + mild: '#FFF5B1', + moderate: '#FFD1AC', + aggressive: '#FDAEB7' + } + }, + spacing: { + '11': '2.75rem', + '14': '3.5rem', + '59': '14.75rem', + '80': '20rem', + '102': '25.5rem', + '128': '32rem' + }, + maxHeight: { + '128': '32rem' + }, + fontFamily: { + sans: [ + 'system-ui', + '-apple-system', + 'BlinkMacSystemFont', + '"Segoe UI"', + 'Roboto', + '"Helvetica Neue"', + 'Arial', + '"Noto Sans"', + 'sans-serif', + '"Apple Color Emoji"', + '"Segoe UI Emoji"', + '"Segoe UI Symbol"', + '"Noto Color Emoji"' + ], + serif: ['Georgia', 'Cambria', '"Times New Roman"', 'Times', 'serif'], + mono: [ + 'Anonymous Pro', + 'Menlo', + 'Monaco', + 'Consolas', + '"Liberation Mono"', + '"Courier New"', + 'monospace' + ] + }, + fontSize: { + xxs: '0.65rem', + '3.2xl': '1.25rem', + '3.25xl': '1.5rem', + '3.5xl': '2rem' + } + } + } +} diff --git a/test/dateFunctions.test.ts b/test/dateFunctions.test.ts new file mode 100644 index 0000000..e2d2261 --- /dev/null +++ b/test/dateFunctions.test.ts @@ -0,0 +1,73 @@ +import {addDays, isValidDate, maxDate, toYYYYMMDD} from '../lib/dateFunctions' + +describe('dateFunctions', () => { + describe('toYYYYMMDD', () => { + for (let i = -11; i <= 12; i++) { + // no matter what time zone we're in, we should return the same date + const mockTzOffset = i * 60 + it(`should handle no arguments (using tz offset ${mockTzOffset})`, () => { + const expectedDate = new Date() + expectedDate.setMinutes(expectedDate.getMinutes() - mockTzOffset) + spyOn(Date.prototype, 'getTimezoneOffset').and.returnValue(mockTzOffset) + expect(toYYYYMMDD()).toBe(expectedDate.toISOString().substring(0, 10)) + }) + + it(`should handle invalid arguments (using tz offset ${mockTzOffset})`, () => { + const expectedDate = new Date() + expectedDate.setMinutes(expectedDate.getMinutes() - mockTzOffset) + spyOn(Date.prototype, 'getTimezoneOffset').and.returnValue(mockTzOffset) + expect(toYYYYMMDD(new Date('hucairz'))).toBe( + expectedDate.toISOString().substring(0, 10) + ) + }) + + it(`should handle an argument (using tz offset ${mockTzOffset})`, () => { + const expectedDate = new Date(0) + const actualDate = toYYYYMMDD(expectedDate) + expect(actualDate).toBe(expectedDate.toISOString().substring(0, 10)) + }) + } + }) + + describe('addDays', () => { + it('should add days to a date', () => { + let date = '2020-02-28' + expect(addDays(date, 1)).toEqual('2020-02-29') + date = '2020-02-29' + expect(addDays(date, 2)).toEqual('2020-03-02') + }) + }) + + describe('isValidDate', () => { + it('should check for a valid dae', () => { + expect(isValidDate('hucairz')).toBe(false) + expect(isValidDate((undefined as unknown) as string)).toBe(false) + expect(isValidDate((null as unknown) as string)).toBe(false) + expect(isValidDate('1234-56-78')).toBe(false) + + expect(isValidDate('2001-09-11')).toBe(true) + }) + }) + + describe('maxDate', () => { + it('should handle empty', () => { + expect(maxDate()).toBe('') + expect(maxDate('')).toBe('') + expect(maxDate('', '')).toBe('') + }) + it('should handle an array of dates', () => { + expect(maxDate('2020-03-01')).toBe('2020-03-01') + expect(maxDate('2020-03-01', '2020-04-01')).toBe('2020-04-01') + expect(maxDate('2020-04-01', '2020-03-01')).toBe('2020-04-01') + expect(maxDate('2020-04-01', '2020-03-01', '2020-03-30')).toBe( + '2020-04-01' + ) + expect( + maxDate('', '2020-04-01', '2020-03-01', '', '2020-03-30', '') + ).toBe('2020-04-01') + }) + }) +}) + +// Avoid tsc from complaining about this file not being a module +export {} diff --git a/test/new-simulation-state.test.ts b/test/new-simulation-state.test.ts new file mode 100644 index 0000000..ed2d252 --- /dev/null +++ b/test/new-simulation-state.test.ts @@ -0,0 +1,337 @@ +import {addDays, toYYYYMMDD} from '../lib/dateFunctions' +import { + getInterventionsEnd, + getNextInterventionPeriodStart, + initializeSimulationState, + Intensity, + NewSimulationState +} from '../lib/new-simulation-state' +import {InterventionMap, Interventions} from '../lib/simulation-types' + +describe('new-simulation-state', () => { + describe('initializeSimulationState', () => { + it('should initialize state with empty interventions', () => { + const state = initializeSimulationState( + createMockRegions(), + createMockInterventions() + ) + expect(state).toEqual({ + interventionPeriods: [], + label: createMockLabel(), + ...createMockRegions() + }) + }) + + it('should initialize state with two interventions of increasing intensity', () => { + const state = initializeSimulationState( + createMockRegions(), + createMockInterventions({ + GathRestrict10: { + dateEnacted: '2020-03-13' + } as any, + StateCurfew: { + dateEnacted: '2020-03-23' + } as any + }) + ) + expect(state).toEqual({ + label: createMockLabel(), + ...createMockRegions(), + interventionPeriods: [ + { + startDate: '2020-03-13', + reductionPopulationContact: 33, + isAutoGenerated: true, + voluntaryHomeQuarantine: Intensity.Aggressive, + caseIsolation: Intensity.Aggressive, + socialDistancing: Intensity.Mild + }, + { + startDate: '2020-03-23', + reductionPopulationContact: 48, + isAutoGenerated: true, + voluntaryHomeQuarantine: Intensity.Aggressive, + caseIsolation: Intensity.Aggressive, + socialDistancing: Intensity.Moderate + } + ] + }) + }) + + it('should initialize state with two interventions second merges with first', () => { + const state = initializeSimulationState( + createMockRegions(), + createMockInterventions({ + GathRestrict10: { + dateEnacted: '2020-03-13' + } as any, + SchoolClose: { + dateEnacted: '2020-03-23' + } as any + }) + ) + expect(state).toEqual({ + label: createMockLabel(), + ...createMockRegions(), + interventionPeriods: [ + { + startDate: '2020-03-13', + reductionPopulationContact: 33, + isAutoGenerated: true, + voluntaryHomeQuarantine: Intensity.Aggressive, + caseIsolation: Intensity.Aggressive, + socialDistancing: Intensity.Mild + }, + { + startDate: '2020-03-23', + reductionPopulationContact: 44, + isAutoGenerated: true, + voluntaryHomeQuarantine: Intensity.Aggressive, + caseIsolation: Intensity.Aggressive, + socialDistancing: Intensity.Mild, + schoolClosure: Intensity.Aggressive + } + ] + }) + }) + + it('should initialize state with two interventions on the same date, second overriding the first', () => { + // multiple periods enacted on same day, just use the most intense. + const state = initializeSimulationState( + createMockRegions(), + createMockInterventions({ + GathRestrict10: { + dateEnacted: '2020-03-13' + } as any, + StateCurfew: { + dateEnacted: '2020-03-13' + } as any + }) + ) + expect(state).toEqual({ + label: createMockLabel(), + ...createMockRegions(), + interventionPeriods: [ + { + startDate: '2020-03-13', + reductionPopulationContact: 48, + isAutoGenerated: true, + voluntaryHomeQuarantine: Intensity.Aggressive, + caseIsolation: Intensity.Aggressive, + socialDistancing: Intensity.Moderate + } + ] + }) + }) + + it('should initialize state with two interventions on the different dates, first overriding the second', () => { + // GathRestrict10 and GathRestrict10 are the same intensity, so our periods have not changed. Just use + // the first period. + const state = initializeSimulationState( + createMockRegions(), + createMockInterventions({ + GathRestrict10: { + dateEnacted: '2020-03-13' + } as any + }) + ) + expect(state).toEqual({ + label: createMockLabel(), + ...createMockRegions(), + interventionPeriods: [ + { + startDate: '2020-03-13', + reductionPopulationContact: 33, + isAutoGenerated: true, + voluntaryHomeQuarantine: Intensity.Aggressive, + caseIsolation: Intensity.Aggressive, + socialDistancing: Intensity.Mild + } + ] + }) + }) + + it('should handle Alabama interventions', () => { + const state = initializeSimulationState( + createMockRegions(), + createMockInterventions(createAlabamaInterventions()) + ) + expect(state).toEqual({ + label: createMockLabel(), + ...createMockRegions(), + interventionPeriods: [ + { + startDate: '2020-03-18', + reductionPopulationContact: 38, + isAutoGenerated: true, + voluntaryHomeQuarantine: 'aggressive', + caseIsolation: 'aggressive', + schoolClosure: 'aggressive' + }, + { + startDate: '2020-03-20', + reductionPopulationContact: 44, + isAutoGenerated: true, + voluntaryHomeQuarantine: 'aggressive', + caseIsolation: 'aggressive', + schoolClosure: 'aggressive', + socialDistancing: 'mild' + }, + { + startDate: '2020-04-04', + reductionPopulationContact: 57, + isAutoGenerated: true, + voluntaryHomeQuarantine: 'aggressive', + caseIsolation: 'aggressive', + schoolClosure: 'aggressive', + socialDistancing: 'moderate' + } + ] + }) + }) + }) + + describe('getNextInterventionPeriodStart', () => { + it('should get start date when there are no interventions', () => { + const today = toYYYYMMDD() + expect(getNextInterventionPeriodStart([])).toBe(today) + }) + + it('should get start date when there are only pre-existing interventions', () => { + const today = toYYYYMMDD() + expect( + getNextInterventionPeriodStart([ + {startDate: addDays(today, -7)} as any, + {startDate: addDays(today, -2)} as any + ]) + ).toBe(today) + }) + + it('should get start date when there are new interventions', () => { + const today = toYYYYMMDD() + expect( + getNextInterventionPeriodStart([ + {startDate: addDays(today, 7)} as any, + {startDate: addDays(today, 20)} as any + ]) + ).toBe(addDays(today, 21)) + }) + }) + + describe('getInterventionsEnd', () => { + it('should get end date when there are no interventions', () => { + const today = toYYYYMMDD() + expect(getInterventionsEnd([])).toBe(addDays(today, 90)) + }) + + it('should get end date when there are only pre-existing interventions', () => { + const today = toYYYYMMDD() + expect( + getInterventionsEnd([ + {startDate: addDays(today, -7)} as any, + {startDate: addDays(today, -2)} as any + ]) + ).toBe(addDays(today, 90)) + }) + + it('should get start date when there are new interventions', () => { + const today = toYYYYMMDD() + expect( + getInterventionsEnd([ + {startDate: addDays(today, 7)} as any, + {startDate: addDays(today, 20)} as any + ]) + ).toBe(addDays(today, 110)) + }) + }) + + function createMockRegions( + regionID = 'US', + subregionID = 'US-AL' + ): Pick { + return { + region: {id: regionID} as any, + subregion: {id: subregionID} as any + } + } + + function createMockLabel() { + return `Simulation created on ${toYYYYMMDD()}` + } + + function createMockInterventions( + interventions: Interventions = {} as any + ): InterventionMap { + return { + US: { + 'US-AL': interventions + } + } + } + + // Actual interventions that was causing an error + function createAlabamaInterventions() { + return { + EmergDec: { + dateIssued: '2020-03-13', + dateEnacted: '2020-03-13', + dateExpiry: '', + dateEnded: '', + notes: 'Public Health Emergency', + source: + 'https://governor.alabama.gov/newsroom/2020/03/third-supplemental-state-of-emergency-coronavirus-covid-19/' + }, + SchoolClose: { + dateIssued: '2020-03-14', + dateEnacted: '2020-03-18', + dateExpiry: '', + dateEnded: '', + notes: + 'in effect 20200318. 20200319 issuance also closed all public/private schools (20200314 is public school)', + source: 'http://alabamapublichealth.gov/legal/assets/420-4-1.13-er.pdf' + }, + GathRestrict25: { + dateIssued: '2020-03-19', + dateEnacted: '2020-03-20', + dateExpiry: '', + dateEnded: '', + notes: 'Announced 20200319, but signed into law 20200320', + source: 'http://alabamapublichealth.gov/legal/assets/420-4-1.13-er.pdf' + }, + GathRestrict10: { + dateIssued: '2020-03-19', + dateEnacted: '2020-03-20', + dateExpiry: '', + dateEnded: '', + notes: 'Announced 20200319, but signed into law 20200320', + source: 'http://alabamapublichealth.gov/legal/assets/420-4-1.13-er.pdf' + }, + OtherBusinessClose: { + dateIssued: '2020-03-27', + dateEnacted: '2020-03-28', + dateExpiry: '2020-04-17', + dateEnded: '', + notes: + 'Non-essential business categories closed included entertainment venues, retail shops, personal care services, and athletic faciltiies. Not considered full NEBusinessClose yet due to only listing of additional types of businsess to close.', + source: 'https://www.alabamapublichealth.gov/news/2020/03/27.html' + }, + RestaurantRestrict: { + dateIssued: '2020-03-19', + dateEnacted: '2020-03-20', + dateExpiry: '', + dateEnded: '', + notes: 'Limited operations required: restaurants, bars, breweries', + source: 'http://alabamapublichealth.gov/legal/assets/420-4-1.13-er.pdf' + }, + StayAtHome: { + dateIssued: '2020-04-03', + dateEnacted: '2020-04-04', + dateExpiry: '2020-04-30', + dateEnded: '', + notes: 'Goes into effect at 5 pm on 20200403', + source: + 'http://www.alabamapublichealth.gov/legal/assets/soe-covid19-stamped-040320.pdf' + } + } + } +}) diff --git a/test/tsconfig.json b/test/tsconfig.json new file mode 100644 index 0000000..5de3cfa --- /dev/null +++ b/test/tsconfig.json @@ -0,0 +1,5 @@ +{ + "compilerOptions": { + "noEmit": true + } +} diff --git a/tsconfig.json b/tsconfig.json new file mode 100644 index 0000000..161e3a7 --- /dev/null +++ b/tsconfig.json @@ -0,0 +1,20 @@ +{ + "compilerOptions": { + "target": "es5", + "module": "esnext", + "strict": true, + "esModuleInterop": true, + "forceConsistentCasingInFileNames": true, + "lib": ["dom", "dom.iterable", "esnext"], + "allowJs": true, + "skipLibCheck": true, + "noEmit": true, + "moduleResolution": "node", + "resolveJsonModule": true, + "isolatedModules": true, + "jsx": "preserve", + "sourceMap": true + }, + "exclude": ["node_modules"], + "include": ["next-env.d.ts", "**/*.ts", "**/*.tsx"] +} diff --git a/types/case-data.ts b/types/case-data.ts new file mode 100644 index 0000000..d9867c8 --- /dev/null +++ b/types/case-data.ts @@ -0,0 +1,12 @@ +/** + * Time series case data + * + * These arrays contain `null` values where case data does not exist for the + * given time. + */ +export type CaseData = { + deaths: (number | null)[] + cumulativeDeaths: (number | null)[] + confirmed: (number | null)[] + cumulativeConfirmed: (number | null)[] +} diff --git a/types/hospital-data.ts b/types/hospital-data.ts new file mode 100644 index 0000000..b5af991 --- /dev/null +++ b/types/hospital-data.ts @@ -0,0 +1,12 @@ +/** + * This data type is for data/hospitals/us.json + */ +export type HospitalData = { + abbr: string + population: number + licensed_beds: number + total_beds: number + icu_beds: number + utilization: number + pct_icu: number +} diff --git a/types/index.d.ts b/types/index.d.ts new file mode 100644 index 0000000..63199ce --- /dev/null +++ b/types/index.d.ts @@ -0,0 +1 @@ +declare module '*.svg' diff --git a/types/model-runner.ts b/types/model-runner.ts new file mode 100644 index 0000000..037f4cc --- /dev/null +++ b/types/model-runner.ts @@ -0,0 +1,149 @@ +// +// Section - Outer request bodies +// + +export interface RequestInput { + id: string | number + models: Model[] + configuration: ModelInput + callbackURL: string | null +} + +export enum RunStatus { + Pending = 'pending', + InProgress = 'in-progress', + Complete = 'complete', + Failed = 'failed' +} + +export interface RunOutput { + modelSlug: ModelSlug + status: RunStatus + resultsLocation: string + exportLocation: string + workflowRunID?: string +} + +// The name of an epidemiological model. +export enum ModelSlug { + MRCIDECovidSim = 'mrc-ide-covid-sim', + Basel = 'basel', + COSMC = 'cosmc' +} + +export interface Model { + slug: ModelSlug + imageURL: string +} + +// +// Section - Model Inputs +// + +/** A generalized description of the input to an epidemiological model. */ +export interface ModelInput { + model: Model + region: string + subregion?: string + parameters: ModelParameters +} + +export interface ModelParameters { + // An ISO-8601 string encoding the date of the most recent death data in the region. + calibrationDate: ISODate + + // The total number of confirmed cases in the region before the calibration date. + calibrationCaseCount: number + + // The total number of deaths in the region before the calibration date. + calibrationDeathCount: number + + // A list of time periods, each with a different set of interventions + interventionPeriods: InterventionPeriod[] + + // r0 override for the virus. If undefined then use the model default + r0: number | null +} + +export interface InterventionPeriod { + // ISO-8601 date when these interventions begin + startDate: ISODate + + // Estimated reduction in population contact + reductionPopulationContact: number + + socialDistancing?: Intensity + schoolClosure?: Intensity + caseIsolation?: Intensity + voluntaryHomeQuarantine?: Intensity +} + +export type ISODate = string + +export enum Intensity { + Mild = 'mild', + Moderate = 'moderate', + Aggressive = 'aggressive' +} + +// +// Section - Model Outputs +// + +export interface ModelOutput { + metadata: ModelInput + binaryHash?: string + time: { + /** The starting date within the model simulation. */ + t0: string + /** + * Timestamps for the series of reported metrics in `regions` and `aggregate`. + * Each timestamp indicates the number of days after `t0`. + */ + timestamps: number[] + /** + * The minimum and maximum timestamps for the series of reported metrics + * in `regions` and `aggregate`. + * Each timestamp indicates the number of days after `t0`. + */ + extent: [number, number] + } + aggregate: { + metrics: SeverityMetrics + } +} + +export type MetricType = + | 'Mild' + | 'ILI' + | 'SARI' + | 'Critical' + | 'CritRecov' + | 'Death' + +export interface SeverityMetrics { + /* Current number of mild cases on this day */ + Mild: number[] + /** Current number of influenza-like illness cases on this day (assume represents GP demand) */ + ILI: number[] + /** Current number of Severe Acute Respiratory Illness cases (assume represents hospital demand) */ + SARI: number[] + /** Current number of critical cases (assume represents ICU demand) */ + Critical: number[] + /** Current number of critical cases who are well enough to be out of ICU but still need a hospital bed */ + CritRecov: number[] + + /** Number of deaths occurring on this day */ + incDeath: number[] + + /** Total number of mild cases since the beginning of the epidemic */ + cumMild: number[] + /** Total number of influence-like illnesses since the beginning of the epidemic */ + cumILI: number[] + /** Total number of severe acute respiratory illnesses since the beginning of the epidemic */ + cumSARI: number[] + /** Total number of critical cases since the beginning of the epidemic */ + cumCritical: number[] + /** Total number of patients recovered from critical cases since the beginning of the epidemic */ + cumCritRecov: number[] +} diff --git a/types/regions.d.ts b/types/regions.d.ts new file mode 100644 index 0000000..d4ab6e1 --- /dev/null +++ b/types/regions.d.ts @@ -0,0 +1,41 @@ +/** + * A mapping of ISO 3166 codes to region specifiers + * + * The length of the code determines alpha-2 vs alpha-3, but we prefer the more + * common alpha-2. + * + * A special subregion ID called "_self" represents the entirety of the region. + * + * https://en.wikipedia.org/wiki/ISO_3166 + */ +export type RegionMap = Record + +/** + * A top-level region, which must have subregions. + */ +export type TopLevelRegion = Region & { + regions: RegionMap +} + +/** + * A region identified by an ISO 3166 + */ +export type Region = { + /** + * The human-readable name of the region + */ + name: string + + /** + * The ISO 3166 code for the region + * + * This may be a 3166-1 or 3166-2 (subregion) dependeing on what level we're + * at. + */ + id: string + + /** + * The subregions of this region + */ + regions?: RegionMap +}