Add web app

.dockerignore

@@ -0,0 +1,3 @@
+*
+!/\.nvmrc
+!/requirements.txt

.gitignore

@@ -17,4 +17,4 @@ __pycache__/
 
 /.snakemake/
 /.vscode/
-.DS_Store
+.DS_Store

.nvmrc

@@ -0,0 +1 @@
+18.14.0

.vercelignore

@@ -0,0 +1,16 @@
+.build
+.cache
+.github
+.ignore
+.reports
+/acknowledgements
+/cluster_tables
+/compare_lineages
+/country_case_data
+/figures
+/other_figures
+/overall_trends_figures
+/plasmid_data
+/travel_data
+docs
+node_modules

CONTRIBUTING.md

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+This document provides some instructions for setting up a development environment for working on the front end of this module.  These steps assume that you are on a Debian/Ubuntu system (I was running Ubuntu 20.04) without any additional Node-related packages installed.  It should not require super-user privileges.
+
+# Installation
+1. Clone this repository and enter the package root with `cd flu_frequencies/web`.
+2. The version of NodeJS provided with Ubuntu 20 is too old (v10.19.0).  To install a newer version that co-exists with the system version, I used [Node Version Manager](https://github.com/nvm-sh/nvm).  Use one of the [installation script](https://github.com/nvm-sh/nvm#install--update-script) provided by the developers.  This creates a hidden directory `.nvm` under `$HOME`.
+   ```console
+   art@Kestrel:~/git/flu_frequencies/web$ curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.3/install.sh | bash
+     % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
+                                    Dload  Upload   Total   Spent    Left  Speed
+   100 15916  100 15916    0     0   353k      0 --:--:-- --:--:-- --:--:--  353k
+   => Downloading nvm from git to '/home/art/.nvm'
+   => Cloning into '/home/art/.nvm'...
+   remote: Enumerating objects: 359, done.
+   remote: Counting objects: 100% (359/359), done.
+   remote: Compressing objects: 100% (305/305), done.
+   remote: Total 359 (delta 40), reused 168 (delta 28), pack-reused 0
+   Receiving objects: 100% (359/359), 219.46 KiB | 13.72 MiB/s, done.
+   Resolving deltas: 100% (40/40), done.
+   * (HEAD detached at FETCH_HEAD)
+     master
+   => Compressing and cleaning up git repository
+
+   => nvm source string already in /home/art/.bashrc
+   => bash_completion source string already in /home/art/.bashrc
+   => Close and reopen your terminal to start using nvm or run the following to use it now:
+
+   export NVM_DIR="$HOME/.nvm"
+   [ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"  # This loads nvm
+   [ -s "$NVM_DIR/bash_completion" ] && \. "$NVM_DIR/bash_completion"  # This loads nvm bash_completion
+   ```
+3. Open a new terminal window so that `$PATH` binary search path includes the `.nvm` directory.
+4. We want to install the Node.js version specified in the hidden `.nvmrc` file.  (Currently the version number is `18.14.0`.)  To automatically install the required version, run `nvm install` and `nvm use`:
+   ```console
+   Downloading and installing node v18.14.0...
+   Downloading https://nodejs.org/dist/v18.14.0/node-v18.14.0-linux-x64.tar.xz...
+   ###################################################################################### 100.0%
+   Computing checksum with sha256sum
+   Checksums matched!
+   Now using node v18.14.0 (npm v9.3.1)
+   Creating default alias: default -> 18.14.0 (-> v18.14.0)
+   ```
+   You can confirm that you are running this new version with the following command:
+   ```console
+   art@Kestrel:~/git/flu_frequencies/web$ which node
+   /home/art/.nvm/versions/node/v18.14.0/bin/node
+   ```
+5. The above step also installs the [Node Package Manager](https://www.npmjs.com/) `npm` in the same local directory.  Install the package dependencies by running `npm install` (if the package manager complains about conflicting dependencies, use a `-force` flag).
+6. Install the [Yarn](https://yarnpkg.com/) package manager: `npm install --global yarn`
+7. Copy the environment variables with `cp .env.example .env`.
+8. Run `yarn install` and `yarn dev` to start the server.
+9. Navigate to `localhost:3000` in your web browser.

data_web/inputs/pathogens.json

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+[
+  {
+    "name": "flu-h3n2",
+    "nameFriendly": "Influenza H3N2",
+    "image": {
+      "file": "images/flu.png",
+      "credit": "Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases (NCIRD)",
+      "source": "https://www.cdc.gov/flu/resource-center/freeresources/graphics/images.htm"
+    },
+    "isEnabled": true,
+    "isVisible": true
+  },
+  {
+    "name": "flu-h1n1pdm",
+    "nameFriendly": "Influenza H1N1pdm",
+    "image": {
+      "file": "images/flu.png",
+      "credit": "Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases (NCIRD)",
+      "source": "https://www.cdc.gov/flu/resource-center/freeresources/graphics/images.htm"
+    },
+    "isEnabled": false,
+    "isVisible": true
+  },
+  {
+    "name": "sars-cov-2",
+    "nameFriendly": "SARS-CoV-2",
+    "image": {
+      "file": "images/sars-cov-2.png",
+      "credit": "Centers for Disease Control and Prevention Newsroom, Image Library",
+      "source": "https://www.cdc.gov/media/subtopic/images.htm"
+    },
+    "isEnabled": false,
+    "isVisible": true
+  },
+  {
+    "name": "monkeypox",
+    "nameFriendly": "Monkeypox",
+    "image": {
+      "file": "images/mpox.png",
+      "credit": "Centers for Disease Control and Prevention Newsroom, Image Library",
+      "source": "https://www.cdc.gov/media/subtopic/images.htm"
+    },
+    "isEnabled": false,
+    "isVisible": true
+  },
+  {
+    "name": "rsv",
+    "nameFriendly": "Respiratory Syncytial Virus (RSV)",
+    "image": {
+      "file": "images/rsv.png",
+      "credit": "Centers for Disease Control and Prevention Newsroom, Public Health Image Library (PHIL)",
+      "source": "https://phil.cdc.gov/Details.aspx?pid=2175"
+    },
+    "isEnabled": false,
+    "isVisible": true
+  }
+]

docker-dev

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+#!/usr/bin/env bash
+
+set -euo pipefail
+
+export NICE="nice -14 ionice -c2 -n3"
+
+DOCKER_REPO="neherlab/flu_frequencies"
+DOCKER_IMAGE_NAME_SAFE="${DOCKER_REPO//\//-}"
+DOCKER_CONTAINER_NAME="${DOCKER_IMAGE_NAME_SAFE}-$(date +%s)"
+
+USER="user"
+GROUP="group"
+
+DEFAULT_COMMAND="cd web && yarn install && yarn dev"
+
+${NICE} docker build -q \
+  --file="docker/docker-dev.dockerfile" \
+  --tag="${DOCKER_REPO}" \
+  --network=host \
+  --build-arg="UID=$(id -u)" \
+  --build-arg="GID=$(id -g)" \
+  --build-arg="USER=${USER}" \
+  --build-arg="GROUP=${GROUP}" \
+  "$(pwd)" >/dev/null
+
+${NICE} docker run -it --rm \
+  --network=host \
+  --init \
+  --name="${DOCKER_CONTAINER_NAME}" \
+  --hostname="${DOCKER_IMAGE_NAME_SAFE}" \
+  --user="$(id -u):$(id -g)" \
+  --volume="$(pwd):/workdir" \
+  --workdir="/workdir" \
+  --env="UID=$(id -u)" \
+  --env="GID=$(id -g)" \
+  --env="USER=${USER}" \
+  --env="GROUP=${GROUP}" \
+  --env="PS1=\${USER}@\${HOST}" \
+  --ulimit core=0 \
+  "${DOCKER_REPO}" \
+  bash -c "set -euo pipefail; ${*:-${DEFAULT_COMMAND}}"

docker/docker-dev.dockerfile

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+# Freeze base image version to
+# ubuntu:20.04 (pushed 2022-06-06T22:39:15.718739Z)
+# https://hub.docker.com/layers/ubuntu/library/ubuntu/20.04/images/sha256-b2339eee806d44d6a8adc0a790f824fb71f03366dd754d400316ae5a7e3ece3e
+FROM ubuntu@sha256:b2339eee806d44d6a8adc0a790f824fb71f03366dd754d400316ae5a7e3ece3e
+
+SHELL ["bash", "-euxo", "pipefail", "-c"]
+
+ARG NODEMON_VERSION="2.0.15"
+ARG YARN_VERSION="1.22.18"
+
+RUN set -euxo pipefail >/dev/null \
+&& export DEBIAN_FRONTEND=noninteractive \
+&& apt-get update -qq --yes \
+&& apt-get install -qq --no-install-recommends --yes \
+  bash \
+  bash-completion \
+  build-essential \
+  ca-certificates \
+  curl \
+  git \
+  gnupg \
+  python3 \
+  python3-pip \
+  python3-setuptools \
+  python3-wheel \
+  sudo \
+  time \
+>/dev/null \
+&& apt-get clean autoclean >/dev/null \
+&& apt-get autoremove --yes >/dev/null \
+&& rm -rf /var/lib/apt/lists/*
+
+ARG USER=user
+ARG GROUP=user
+ARG UID
+ARG GID
+
+ENV USER=$USER
+ENV GROUP=$GROUP
+ENV UID=$UID
+ENV GID=$GID
+ENV TERM="xterm-256color"
+ENV HOME="/home/${USER}"
+ENV NODE_DIR="/opt/node"
+ENV PATH="${NODE_DIR}/bin:${HOME}/.local/bin:${PATH}"
+
+# Install Node.js
+COPY .nvmrc /
+RUN set -eux >dev/null \
+&& mkdir -p "${NODE_DIR}" \
+&& cd "${NODE_DIR}" \
+&& NODE_VERSION=$(cat /.nvmrc) \
+&& curl -fsSL  "https://nodejs.org/dist/v${NODE_VERSION}/node-v${NODE_VERSION}-linux-x64.tar.xz" | tar -xJ --strip-components=1 \
+&& npm install -g nodemon@${NODEMON_VERSION} yarn@${YARN_VERSION} >/dev/null
+
+#&& npm config set scripts-prepend-node-path auto
+
+# Calm down the (in)famous chatter from yarn
+RUN set -euxo pipefail >/dev/null \
+&& sed -i'' "s/this.reporter.warn(this.reporter.lang('incompatibleResolutionVersion', pattern, reqPattern));//g" "${NODE_DIR}/lib/node_modules/yarn/lib/cli.js" \
+&& sed -i'' "s/_this2\.reporter.warn(_this2\.reporter.lang('ignoredScripts'));//g" "${NODE_DIR}/lib/node_modules/yarn/lib/cli.js" \
+&& sed -i'' 's/_this3\.reporter\.warn(_this3\.reporter\.lang(peerError.*;//g' "/opt/node/lib/node_modules/yarn/lib/cli.js"
+
+
+# Install Python dependencies
+COPY requirements.txt /
+RUN set -euxo pipefail >/dev/null \
+&& pip3 install --user -r /requirements.txt
+
+
+# Make a user and group
+RUN set -euxo pipefail >/dev/null \
+&& \
+  if [ -z "$(getent group ${GID})" ]; then \
+    addgroup --system --gid ${GID} ${GROUP}; \
+  else \
+    groupmod -n ${GROUP} $(getent group ${GID} | cut -d: -f1); \
+  fi \
+&& \
+  if [ -z "$(getent passwd ${UID})" ]; then \
+    useradd \
+      --system \
+      --create-home --home-dir ${HOME} \
+      --shell /bin/bash \
+      --gid ${GROUP} \
+      --groups sudo \
+      --uid ${UID} \
+      ${USER}; \
+  fi \
+&& sed -i /etc/sudoers -re 's/^%sudo.*/%sudo ALL=(ALL:ALL) NOPASSWD: ALL/g' \
+&& sed -i /etc/sudoers -re 's/^root.*/root ALL=(ALL:ALL) NOPASSWD: ALL/g' \
+&& sed -i /etc/sudoers -re 's/^#includedir.*/## **Removed the include directive** ##"/g' \
+&& echo "foo ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers \
+&& touch ${HOME}/.hushlogin \
+&& chown -R ${UID}:${GID} "${HOME}"
+
+USER ${USER}

infra/data/lambda-at-edge/OriginRequest.lambda.js

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+/* eslint-disable prefer-destructuring,sonarjs/no-collapsible-if,unicorn/no-lonely-if */
+// Implements rewrite of non-compressed to .gz URLs using AWS
+// Lambda@Edge. This is useful if you have precompressed your files.
+//
+// Usage:
+// Create an AWS Lambda function and attach it to "Origin Request" event of a
+// Cloudfront distribution
+
+const ARCHIVE_EXTS = ['.7z', '.br', '.bz2', '.gz', '.lzma', '.xz', '.zip', '.zst']
+
+function getHeader(headers, headerName) {
+  const header = headers[headerName.toLowerCase()]
+  if (!header || !header[0] || !header[0].value) {
+    return undefined
+  }
+  return header[0].value
+}
+
+function acceptsEncoding(headers, encoding) {
+  const ae = getHeader(headers, 'Accept-Encoding')
+  if (!ae || typeof ae != 'string') {
+    return false
+  }
+  return ae.split(',').some((e) => e.trim().toLowerCase().startsWith(encoding.toLowerCase()))
+}
+
+function handler(event, context, callback) {
+  const request = event.Records[0].cf.request
+  const headers = request.headers
+
+  // If not an archive file (which are not precompressed), rewrite the URL to
+  // get the corresponding .gz file
+  if (ARCHIVE_EXTS.every((ext) => !request.uri.endsWith(ext))) {
+    if (acceptsEncoding(headers, 'gzip')) {
+      request.uri += '.gz'
+    }
+  }
+
+  callback(null, request)
+}
+
+exports.handler = handler

infra/data/lambda-at-edge/ViewerResponse.lambda.js

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+// Adds additional headers to the response, including security headers and CORS.
+// Suited for serving data and APIs.
+//
+// See also:
+//  - https://securityheaders.com/
+//
+// Usage: Create an AWS Lambda@Edge function and attach it to "Viewer Response"
+// event of a Cloudfront distribution
+
+const NEW_HEADERS = {
+  'Access-Control-Allow-Origin': '*',
+  'Access-Control-Allow-Methods': 'GET, OPTIONS',
+  'Content-Security-Policy': `default-src 'none'; frame-ancestors 'none'`,
+  'Strict-Transport-Security': 'max-age=15768000; includeSubDomains; preload',
+  'X-Content-Type-Options': 'nosniff',
+  'X-DNS-Prefetch-Control': 'off',
+  'X-Download-Options': 'noopen',
+  'X-Frame-Options': 'DENY',
+  'X-XSS-Protection': '1; mode=block',
+}
+
+function addHeaders(headersObject) {
+  return Object.fromEntries(
+    Object.entries(headersObject).map(([header, value]) => [header.toLowerCase(), [{ key: header, value }]]),
+  )
+}
+
+const HEADERS_TO_REMOVE = new Set(['server', 'via'])
+
+function filterHeaders(headers) {
+  return Object.entries(headers).reduce((result, [key, value]) => {
+    if (HEADERS_TO_REMOVE.has(key.toLowerCase())) {
+      return result
+    }
+
+    if (key.toLowerCase().includes('powered-by')) {
+      return result
+    }
+
+    return { ...result, [key.toLowerCase()]: value }
+  }, {})
+}
+
+function modifyHeaders({ response }) {
+  let newHeaders = addHeaders(NEW_HEADERS)
+
+  newHeaders = {
+    ...response.headers,
+    ...newHeaders,
+  }
+
+  newHeaders = filterHeaders(newHeaders)
+
+  return newHeaders
+}
+
+exports.handler = (event, context, callback) => {
+  const { request, response } = event.Records[0].cf
+  response.headers = modifyHeaders({ request, response })
+  callback(null, response)
+}
+
+exports.modifyHeaders = modifyHeaders

infra/find-lambda-at-edge-logs.sh

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Inspired by https://stackoverflow.com/a/54096479/526860
+
+FUNCTION_NAME=$1
+
+for region in $(aws --output text ec2 describe-regions | cut -f 4); do
+  for loggroup in $(aws --output text logs describe-log-groups --log-group-name "/aws/lambda/us-east-1.$FUNCTION_NAME" --region $region --query 'logGroups[].logGroupName'); do
+    printf "$region\tconsole.aws.amazon.com/cloudwatch/home?region=$region#logsV2:log-groups/log-group/\$252Faws\$252Flambda\$252Fus-east-1.$FUNCTION_NAME\n"
+  done
+done