Move non-entrypoint JavaScript into src/

While there may have been some rhyme or reason for creating these files
outside of src/ originally, it's no longer apparent.  It's nice to
systematize the file organization a bit, esp. in advance of additional
files I'm planning to add to support new server-side API endpoints.

README.md

@@ -79,7 +79,7 @@ Nextstrain documentation is hosted by Read The Docs at [docs.nextstrain.org](htt
 Please see [this GitHub repo](https://github.com/nextstrain/docs.nextstrain.org/) 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](https://github.com/nextstrain/nextstrain.org/pull/226).
-A number of [redirects](./redirects.js) have been added to preserve old URLs.
+A number of [redirects](./src/redirects.js) have been added to preserve old URLs.
 
 ---
 ## Auspice client

docs/infrastructure.md

@@ -26,7 +26,7 @@ Deploys of `master` happen automatically after Travis CI tests are successful.
 
   - `REDIS_URL` is provided by the Heroku Redis add-on.
     It should not be modified directly.
-    Our [authentication handlers](../authn.js) rewrite it at server start to use a secure TLS connection.
+    Our [authentication handlers](../src/authn/index.js) rewrite it at server start to use a secure TLS connection.
 
   - `FETCH_CACHE` is not currently used, but can be set to change the location of the on-disk cache used by (some) server `fetch()`-es.
     The default location is `/tmp/fetch-cache`.
@@ -107,7 +107,7 @@ Ephemeral instances are automatically managed by AWS Batch for `nextstrain build
 ## Cognito
 
 A [_user pool_](https://docs.aws.amazon.com/cognito/latest/developerguide/cognito-user-identity-pools.html) called `nextstrain.org` provides authentication for Nextstrain logins.
-Cognito is integrated with the nextstrain.org server using the OAuth2 support from PassportJS in our [`authn.js`](../authn.js) file.
+Cognito is integrated with the nextstrain.org server using the OAuth2 support from PassportJS in our [`authn/index.js`](../src/authn/index.js) file.
 
 We currently don't use Cognito's [_identity pools_](https://docs.aws.amazon.com/cognito/latest/developerguide/cognito-identity.html).
 It may be beneficial to use one in the future so we can get temporary AWS credentials specific to each Nextstrain user with the appropriate authorizations baked in (instead of using a server-wide set of credentials).

server.js

@@ -8,7 +8,7 @@ const favicon = require('serve-favicon');
 const compression = require('compression');
 const argparse = require('argparse');
 const utils = require("./src/utils");
-const { potentialAuspiceRoutes, isRequestBackedByAuspiceDataset } = require('./auspicePaths');
+const { potentialAuspiceRoutes, isRequestBackedByAuspiceDataset } = require('./src/auspicePaths');
 const cors = require('cors');
 const {addAsync} = require("@awaitjs/express");
 const {NotFound} = require('http-errors');
@@ -37,8 +37,8 @@ global.verbose = args.verbose;
 // Import these after parsing CLI arguments and setting global.verbose so code
 // in them can use utils.verbose() at load time.
 const auspiceServerHandlers = require("./src/index.js");
-const authn = require("./authn");
-const redirects = require("./redirects");
+const authn = require("./src/authn");
+const redirects = require("./src/redirects");
 
 /* Path helpers for static assets, to make routes more readable.
  */

auspicePaths.js → src/auspicePaths.js

@@ -1,7 +1,7 @@
 const fetch = require("node-fetch");
-const sources = require("./src/sources");
-const { warn } = require("./src/utils");
-const { splitPrefixIntoParts, parsePrefix } = require("./src/getDatasetHelpers");
+const sources = require("./sources");
+const { warn } = require("./utils");
+const { splitPrefixIntoParts, parsePrefix } = require("./getDatasetHelpers");
 
 /**
  * Auspice core builds have URLs where the first (`/`-separated) field matches the following list.

authn.js → src/authn/index.js

@@ -11,9 +11,9 @@ const OAuth2Strategy = require("passport-oauth2").Strategy;
 const {jwtVerify} = require('jose/jwt/verify');                   // eslint-disable-line import/no-unresolved
 const {createRemoteJWKSet} = require('jose/jwks/remote');         // eslint-disable-line import/no-unresolved
 const {JOSEError, JWTClaimValidationFailed} = require('jose/util/errors');   // eslint-disable-line import/no-unresolved
-const BearerStrategy = require("./src/authn/bearer");
-const sources = require("./src/sources");
-const utils = require("./src/utils");
+const BearerStrategy = require("./bearer");
+const sources = require("../sources");
+const utils = require("../utils");
 
 const PRODUCTION = process.env.NODE_ENV === "production";
 

redirects.js → src/redirects.js

@@ -1,6 +1,6 @@
 const url = require('url');
-const helpers = require("./src/getDatasetHelpers");
-const { parseNarrativeLanguage } = require("./src/utils");
+const helpers = require("./getDatasetHelpers");
+const { parseNarrativeLanguage } = require("./utils");
 
 const setup = (app) => {
 

static-site/gatsby-config.js

@@ -1,6 +1,6 @@
 const { createProxyMiddleware } = require("http-proxy-middleware");
 const config = require("./data/SiteConfig");
-const {potentialAuspiceRoutes} = require("../auspicePaths");
+const {potentialAuspiceRoutes} = require("../src/auspicePaths");
 
 // const pathPrefix = config.pathPrefix === "/" ? "" : config.pathPrefix;
 

test/unit/routing.test.js

@@ -1,4 +1,4 @@
-const {isRequestBackedByAuspiceDataset} = require("../../auspicePaths.js");
+const {isRequestBackedByAuspiceDataset} = require("../../src/auspicePaths.js");
 
 jest.setTimeout(10000);