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Nextstrain.org

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Our goal is to aid epidemiological understanding and improve outbreak response. If you have any questions, or simply want to say hi, please give us a shout at hello@nextstrain.org or introduce yourself at discussion.nextstrain.org.

We have received a number of generous offers to contribute front-end developer effort to nextstrain (and auspice) folowing our work on SARS-CoV-2. We would be grateful for code contributions, as well as constructive criticism and advice. A list of potential issues is being actively maintained at https://github.com/orgs/nextstrain/projects/5.

This repo comprises:

1. A server (./server.js) which serves all the content on nextstrain.org, handles authentication and responds to API requests.
2. The splash & documentation pages, which are built using Gatsby & located in the ./static-site directory.
3. Code to build a customised version of the Auspice client, which is located in the ./auspice-client directory.

This repository provides the tools you need to build nextstrain.org locally and deploy nextstrain.org.

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Build nextstrain.org locally

1. Install prerequisites

Install the node dependencies by running

npm ci

from this directory (the "nextstrain.org" directory).

Using npm ci instead of npm install ensures your dependency tree matches those in package-lock.json.

2. Build the site

npm run build runs ./build.sh to build both the static site & an auspice client with customisations. The following section details the different ways to serve these pages on a local server after building the site.

3. Run server

Run server mirroring the deployed (live) website

npm run server will start a local server, by default available at localhost:5000. This should mirror exactly what you see when you visit nextstrain.org. In order to replicate the live behavior, you will need the appropriate environment variables set (see below).

Run server in development mode

If you are developing on nextstrain.org, we recommend running:

npm run dev , which runs ./develop.sh to launch a development server of nextstrain.org, by default available at localhost:8000. Changes to files in ./static-site will be reflected in the corresponding pages on the development server without needing to refresh.

This works by running the main nextstrain server on port 5000 and then running the Gatsby (see below for more on Gatsby) server on port 8000 and directing requests outside of Gatsby to port 5000. See nextstrain.org/pull/280 for more on this.

An alternative approach is to build the site (as above) and then start the server:

NODE_ENV="dev" npm run server

Environment variables

See docs/infrastructure.md for a description of the environment variables used by the server. For running locally, you should ensure

• NODE_ENV is not set to "production", as authentication will not work on localhost.
• AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY are a valid AWS IAM user, in order for the server to access S3 buckets. Alternatively, these may be configured using ~/.aws/credentials. If you add a new profile to ~/.aws/credentials, you can then tell the server to use it by setting AWS_PROFILE=....

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Splash page (and other misc pages)

There are a number of pages built using Gatsby and found in ./static-site/. See static-site/README.md for instructions on how to add content and develop this portion of the site in isolation. In production, these are compiled (npm run build) and served via the nextstrain.org server (npm run server).

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Documentation

Nextstrain documentation is hosted by Read The Docs at docs.nextstrain.org. Please see this GitHub repo for more details.

Note that the documentation used to be served from the server in this repo at URLs such as nextstrain.org/docs/... until November 2020. A number of redirects have been added to preserve old URLs.

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Auspice client

We use Auspice to visualise & interact with phylogenomic data.

A customised version of the Auspice client

We build a customised version of the auspice client (e.g. the part you see in the browser) for nextstrain.org. The auspice customisations specific to nextstrain.org are found in ./auspice-client/customisations/. Please see the auspice documentation for more information on customising auspice.

Testing locally

Make sure you've installed dependencies with npm ci first (and activated your conda environment if using one).

If you have AWS credentials make sure they are set as environment variables (AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY). These are not necessary, but some functionality will be missing if these aren't available.

Then run:

./build.sh auspice
npm run server

This will create the auspice-client/index.html and auspice-client/dist/* files which are gitignored. Note that the favicon.png isn't needed for auspice, as the nextstrain.org server handles this.

You can also run Auspice's own development server (not the nextstrain.org server) to ease development of client customizations. This means that you will see a different splash page & the documentation will not work. It is not currently possible to run auspice in development mode & see the nextstrain.org splash page & docs. Read the section below on the nextstrain.org server for more context.

cd auspice-client
npx auspice develop --verbose --extend ./customisations/config.json --handlers ../src/index.js

If you're not familiar with npx, it's a command to easily run programs installed by npm. Running npx auspice above is equivalent to ../node_modules/.bin/auspice.

Using a different version of Auspice

Sometimes it is useful to change the version of Auspice that is used. Perhaps you're upgrading the version nextstrain.org uses or you want to test changes in a local copy of Auspice against nextstrain.org.

If you're upgrading the version of Auspice used, install the new version with npm install auspice@.... Replace ... with the semantic version specifier you want. This will change package.json and package-lock.json to reflect the new version you installed. When preparing to commit your Auspice version change, you'll want to include those changed files too. Run npx auspice --version to check that (a) it's installed correctly and (b) which version you have.

Then build and run the server as above with either:

./build.sh auspice
npm run server

or

cd auspice-client
npx auspice develop --verbose --extend ./customisations/config.json --handlers ../src/index.js

If you're installing from a local development copy of Auspice's source, you can use npm link to use your local copy without the need to continually re-install it after every change:

npm link <path to auspice repo>
npm link <path to auspice repo>/node_modules/react

This uses symlinks both globally and within the local node_modules/ directory to point the local Auspice dependency to your local Auspice source.

Using npm install <path to auspice repo> will not work to use a local development copy, as dependencies are handled differently with npm install vs. npm link in this case.

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Nextstrain.org server

npm run server runs ./server.js which serves all the content on nextstrain.org & handles authentication.

This server decides based on the path, whether to serve:

• the bundled auspice JavaScript file (i.e. the auspice client, built above via ./build.sh auspice) or
• the (pre-built) static splash & documentation pages

Aside: How do auspice (client) - server communications work?

Auspice is a flexible tool created for visualising phylogenomic data that are not specific to any domain. It can make the following API requests to a server:

• /charon/getAvailable
• /charon/getNarrative
• /charon/getDataset and as long as there is a server and the reponse is appropriate then the auspice client can visualise the data.

The nextstrain.org server (server.js) sets up GET request handlers for those three endpoints using code imported from ./src/index.js.

The code for these handlers, which is exposed by ./src/index.js, has been written in such a way that it can be imported by:

1. The nextstrain.org server: npm run server (see server.js)
2. The auspice server: cd auspice-client && npx auspice view --handlers ../src/index.js --verbose (rarely useful in this case, make sure you've run npm run build -- auspice first!)
3. The auspice development server: npx auspice develop --handlers ./src/index.js --verbose --extend ./auspice-client/customisations/config.json (useful for auspice development, note the client customisations applied here too!)

Note that 2 and 3 are running the auspice server locally but modifying it via functionality whereby the default request handlers (for /charon/... GET requests) can be overwritten by command line arguments. In this case, they're overwriting them with the handlers used by the nextstrain.org server (see server.js) and thus the auspice server mimics the nextstrain.org server behavior (fetching datasets from S3, etc.). See the auspice API documentation for more info.

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Deployments

See the infrastructure documentation for details.

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Testing

Nextstrain.org currently implements limited smoke-testing to test requests originiating from the Auspice client to the nextstrain.org server (i.e. API GET requests starting with /charon/). These are defined in this JSON file and can be run via

npm run test:ci

Which will run a local server for the duration of the tests. Alternatively, you can run your own server in the background and run npm run smoke-test.

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