Influenza page #271

this fetches the sars-cov-2 build catalogue from s3 instead of using a local version. it also refactors the react components behind /sars-cov-2 to be more flexible for other pathogen pages like /influenza.

this directory contains components which are now generally applicable to any page that wants to display a collection of info about any grouping of builds (e.g. flu, groups, commeunity), not just for sars-cov-2.

in anticipation of using it for any listing of builds, not specific to sars-cov-2. This picks up where that left off in anticipation of using it for a flu builds page. Specifically this commit allows the build hierarchy to be defined by custom field names in a build catalogue yaml (e.g. static-site/content/allSARS-CoV-2Builds.yaml) . These field names are passed to the builds component so it can create the hierarchy according to them.

This creates a page at /influenza analogous to /sars-cov-2 but for flu. Note that this page isn't called /flu because of conflict with existing redirects. In addition to creating a useful hub for gathering resources about flu, this can serve as an example of how it should hopefully now be easier to create more pages like this that show off all that Nextstrain has to offer on a particular pathogen or topic spanning pathogens (e.g. a /groups page that lists all nextstrain groups and links to docs about groups etc). In many cases these pages can serve as a way to dedicate more UI real estate to some things or sections we show off on the splash page and offer a more customized landing page for a particular topic.

Decouple build map from build dropdown menu. Remove spacers and non-specific stuff from specific components like hierarchical dropdown menu and sit-rep listing. Decouple fetching of build catalogue from dropdown menu.

1: Flatten hierarchy in anticipation of flatter UI. 2: Manually add properties for easy parsing in react. The long-term solution here will be to generate things like this by parsing build URLs in collect-pathogen-resources.js

this offers an alternative way to list builds that is more flexible - listing them in a flat (non-hierarchical) interface that can be filtered. The listing can easily be converted into a table or other. see #62 (comment) for more details

to be changed back. just so we can test in dev apps on github PRs etc

This commit streamlines the dataset selection UI to use generic keywords from filenames. Principally, it: 1. Creates a new light weight collect-datasets.js script from collect-pathogen-resources.js that provisions datasets_influenza.json 2. Modifies influenza.jsx to use this dataset listing 3. Creates a new DatasetSelect component from FilterBuilds that filters by keyword and that implements some row styling

This uses react-styled-flexboxgrid for a responsive grid layout. We use Bootstrap elsewhere in nextstrain.org to accomplish a similar outcome, however, Bootstrap css and className="col-md-1" don't interact well with the use of styled-components. Here, I've opted for a Flexbox solution. This adds a dependency to package.json, but allows for an easy, expressive grid and I think should be generally useful. I compared a few similar options for this and this one was my favorite.

update https://data.nextstrain.org/datasets_influenza.json every 5 minutes with s3 flu datasets

#279 gives more flexibility by depending on the output of scripts/collect-datasets.js instead and using a more scalable UI

an earlier commit on this branch changed this component to fetch the sars-cov-2 builds catalogue that backs /sars-cov-2 from s3. This changes back to the original way of using a local YAML file instead, because we are holding off on the s3 implementation for now.

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Influenza page #271

Influenza page #271

Commits on Mar 11, 2021