Merge pull request #226 from nextstrain/migrate-docs

Redirect /docs and /help to docs.nextstrain.org

README.md

@@ -40,11 +40,20 @@ You'll need AWS credentials configured (via environment or `~/.aws/credentials`)
 If you add a new profile to `~/.aws/credentials`, you can then tell the local nextstrain.org server to use it by setting `AWS_PROFILE=...`.
 
 ---
-## Splash & documentation pages
-These are found in `./static-site/`.
-See [static-site/README.md](./static-site/README.md) for instructions on how to add content (e.g. docs) and develop this portion of the site in isolation.
-In production, this is built using Gatsby (`npm run build`) and served via the nextstrain.org server (`npm run server`).
 
+## 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](./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`).
+
+---
+## Documentation
+
+Nextstrain documentation is hosted by Read The Docs at [docs.nextstrain.org](https://docs.nextstrain.org).
+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 nextstain.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.
 
 ---
 ## Auspice client

auspice-client/customisations/navbar.js

@@ -59,9 +59,9 @@ const getStyles = ({minified=true, width}={}) => ({
   }
 });
 
-const renderLink = (text, url, style) => (
-  <a key={text} style={style} href={url}>
-    {text}
+const Link = (props) => (
+  <a key={props.text} href={props.href} style={props.style} target={props.target} rel={props.rel}>
+    {props.text}
   </a>
 );
 
@@ -92,8 +92,8 @@ class WhoAmI extends React.Component {
     return (
       <div>
         { this.state.user
-          ? renderLink(`👤 ${this.state.user.username}`, "/whoami", styles.link)
-          : renderLink("LOGIN", "/login", styles.link) }
+          ? <Link text={`👤 ${this.state.user.username}`} href="/whoami" style={styles.link}/>
+          : <Link text="LOGIN" href="/login" style={styles.link}/> }
       </div>
     );
   }
@@ -123,8 +123,8 @@ const NavBar = ({sidebar, narrativeTitle, width}) => {
           null : (
             <div style={{...styles.flexColumns, paddingRight: "12px"}}>
               <div style={{flex: 5}}/>
-              {renderLink("DOCS", "/docs", styles.link)}
-              {renderLink("HELP", "/help", styles.link)}
+              <Link href="https://docs.nextstrain.org/en/latest/index.html" style={styles.link} text="DOCS"/>
+              <Link href="https://docs.nextstrain.org/en/latest/learn/about-nextstrain.html" style={styles.link} text="HELP"/>
               <WhoAmI sidebar={sidebar}/>
             </div>
           )

package.json

@@ -43,6 +43,7 @@
     "passport": "^0.4.0",
     "passport-oauth2": "^1.5.0",
     "query-string": "^4.2.3",
+    "react-icons": "^3.11.0",
     "request": "^2.88.0",
     "serve-favicon": "^2.5.0",
     "session-file-store": "^1.3.1",

redirects.js

@@ -3,9 +3,9 @@ const { parseNarrativeLanguage } = require("./src/utils");
 
 const setup = (app) => {
 
-  /* send auspice to the auspice docs (currently hosted as github pages) */
+  /* send auspice to the auspice docs (currently hosted on docs.nextstrain.org) */
   app.route("/auspice")
-    .get((req, res) => res.redirect('https://nextstrain.github.io/auspice/'));
+    .get((req, res) => res.redirect('https://docs.nextstrain.org/projects/auspice/en/latest/'));
 
   /* we don't yet have a community page */
   app.route("/community")
@@ -52,6 +52,72 @@ const setup = (app) => {
   conflates a language part ("zh") with a region ("europe") so we want to keep zh out of the manifest JSON */
   app.route("/ncov/zh").get((req, res) => res.redirect("/ncov/global/zh"));
 
+  /**
+   * DOCS & HELP Redirects
+   * In November 2020 we shifted the docs from being hosted by this server
+   * at nextstrain.org/docs and nextstrain.org/help
+   * to a Read The Docs setup running at docs.nextstrain.org.
+   * This block contains the appropriate redirects
+   */
+  const mainReadTheDocs = "https://docs.nextstrain.org/en/latest";
+  const augurReadTheDocs = "https://docs.nextstrain.org/projects/augur/en/latest";
+  const docsRedirects = {
+    "/docs": `${mainReadTheDocs}`,
+    "/help": `${mainReadTheDocs}/learn/about-nextstrain.html`,
+    "/docs/getting-started/introduction": `${mainReadTheDocs}/learn/about-nextstrain.html`,
+    "/about": `${mainReadTheDocs}/learn/about-nextstrain.html`,
+    "/about/overview/introduction": `${mainReadTheDocs}/learn/about-nextstrain.html`,
+    "/about/overview": `${mainReadTheDocs}/learn/about-nextstrain.html`,
+    "/about/methods/introduction": `${mainReadTheDocs}/learn/about-nextstrain.html`,
+    "/about/methods": `${mainReadTheDocs}/learn/about-nextstrain.html`,
+    "/docs/getting-started/local-installation": `${mainReadTheDocs}/guides/install/local-installation.html`,
+    "/docs/getting-started/installation": `${mainReadTheDocs}/guides/install/local-installation.html`,
+    "/docs/getting-started/local-vs-container-install": `${mainReadTheDocs}/guides/install/index.html`,
+    "/docs/getting-started/container-installation": `${mainReadTheDocs}/guides/install/cli-install.html`,
+    "/docs/getting-started/quickstart": `${mainReadTheDocs}/tutorials/quickstart.html`,
+    "/docs/getting-started/windows-help": `${mainReadTheDocs}/guides/install/windows-help.html`,
+    "/docs/bioinformatics/introduction-to-augur": `${augurReadTheDocs}/index.html`,
+    "/docs/bioinformatics/introduction": `${augurReadTheDocs}/faq/index.html`,
+    "/docs/bioinformatics/what-is-a-build": `${augurReadTheDocs}/faq/what-is-a-build.html`,
+    "/docs/bioinformatics/data-formats": `${mainReadTheDocs}/reference/formats/data-formats.html`,
+    "/docs/bioinformatics/output-jsons": `${mainReadTheDocs}/reference/formats/data-formats.html`,
+    "/docs/bioinformatics/augur-commands": `${augurReadTheDocs}/usage/cli/cli.html`,
+    "/docs/bioinformatics/customizing-a-build": `${mainReadTheDocs}/guides/bioinformatics/index.html`,
+    "/docs/tutorials/defining-clades": `${mainReadTheDocs}/guides/bioinformatics/defining-clades.html`,
+    "/docs/tutorials/zika": `${mainReadTheDocs}/tutorials/zika.html`,
+    "/docs/getting-started/zika-tutorial": `${mainReadTheDocs}/tutorials/zika.html`,
+    "/docs/tutorials/tb": `${mainReadTheDocs}/tutorials/tb_tutorial.html`,
+    "/docs/getting-started/tb-tutorial": `${mainReadTheDocs}/tutorials/tb_tutorial.html`,
+    "/docs/contributing/community-builds": `${mainReadTheDocs}/guides/share/community-builds.html`,
+    "/docs/contributing/documentation": `${mainReadTheDocs}/guides/contribute/documentation.html`,
+    "/docs/contributing/development": `${mainReadTheDocs}/guides/contribute/index.html`,
+    "/docs/contributing/fetch-data-from-custom-urls": `${mainReadTheDocs}/guides/share/fetch-via-urls.html`,
+    "/fetch": `${mainReadTheDocs}/guides/share/fetch-via-urls.html`,
+    "/docs/contributing/nextstrain-groups": `${mainReadTheDocs}/guides/share/nextstrain-groups.html`,
+    "/docs/contributing/sharing-data": `${mainReadTheDocs}/guides/share/index.html`,
+    "/docs/contributing/philosophy": `${mainReadTheDocs}/guides/share/index.html`,
+    "/docs/visualisation/download-data": `${mainReadTheDocs}/guides/share/download-data.html`,
+    "/docs/visualisation/map-interpretation": `${mainReadTheDocs}/learn/interpret/map-interpretation.html`,
+    "/docs/visualisation/narratives": `${mainReadTheDocs}/guides/communicate/narratives-intro.html`,
+    "/docs/narratives/introduction": `${mainReadTheDocs}/guides/communicate/narratives-intro.html`,
+    "/help/general/about-nextstrain": `${mainReadTheDocs}/learn/about-nextstrain.html`,
+    "/help/general/how-to-read-a-tree": `${mainReadTheDocs}/learn/interpret/how-to-read-a-tree.html`,
+    "/help/general/interacting-with-nextstrain": `${mainReadTheDocs}/learn/interpret/interacting-with-nextstrain.html`,
+    "/docs/interpretation": `${mainReadTheDocs}/learn/interpret/index.html`,
+    "/docs/interpretation/auspice": `${mainReadTheDocs}/learn/interpret/index.html`,
+    "/docs/visualisation": `${mainReadTheDocs}/learn/interpret/index.html`,
+    "/docs/visualisation/introduction": `${mainReadTheDocs}/learn/interpret/index.html`,
+    "/help/coronavirus/FAQ": `${mainReadTheDocs}/learn/pathogens/coronavirus/FAQ.html`,
+    "/help/coronavirus/SARS-CoV-2": `${mainReadTheDocs}/learn/pathogens/coronavirus/SARS-CoV-2.html`,
+    "/help/coronavirus/Technical-FAQ": `${mainReadTheDocs}/learn/pathogens/coronavirus/Technical-FAQ.html`,
+    "/help/coronavirus/human-CoV": `${mainReadTheDocs}/learn/pathogens/coronavirus/human-CoV.html`
+  };
+
+  for (const [from, to] of Object.entries(docsRedirects)) {
+    app.route([from])
+      .get((req, res) => res.redirect(to));
+  }
+
 };
 
 module.exports = {

static-site/additional_sidebar_entries.yaml

@@ -6,43 +6,10 @@
 # (for me) to do it on the react side as that's where i'm more
 # comfortable.
 #                                                   james, June 2020.
-- section: "docs"
-  chapter: "getting-started"
-  name: "Container Installation"
-  url: "https://docs.nextstrain.org/projects/cli/en/latest/installation/"
-- section: "docs"
-  chapter: "tutorials"
-  name: "Analysing MTb (VCF) data"
-  url: "https://docs.nextstrain.org/projects/augur/en/stable/tutorials/tb_tutorial.html"
-- section: "docs"
-  chapter: "tutorials"
-  name: "Analysing SARS-CoV-2 data"
-  url: "https://nextstrain.github.io/ncov/"
-- section: "docs"
-  chapter: "bioinformatics"
-  name: "Augur Commands"
-  url: "https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/cli.html"
-- section: "docs"
-  chapter: "bioinformatics"
-  name: "Frequently Asked Questions"
-  url: "https://docs.nextstrain.org/projects/augur/en/stable/faq/faq.html"
-- section: "docs"
-  chapter: "tutorials"
-  name: "Writing a Narrative"
-  url: "https://nextstrain.github.io/auspice/narratives/how-to-write"
-- section: "docs"
-  chapter: "contributing"
-  name: "Development"
-  url: "https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md"
-- section: "docs"
-  chapter: "visualisation"
-  name: "Interactive Narratives"
-  url: "https://nextstrain.github.io/auspice/narratives/introduction"
-- section: "docs"
-  chapter: "visualisation"
-  name: "Drag & Drop Metadata"
-  url: "https://nextstrain.github.io/auspice/advanced-functionality/drag-drop-csv-tsv"
-- section: "docs"
-  chapter: "visualisation"
-  name: "Display Multiple Trees"
-  url: "https://nextstrain.github.io/auspice/advanced-functionality/second-trees"
+# After migrating all docs to docs.nextstrain.org, we no longer use this.
+#                                                   eli, October 2020.
+# Here is what it would look like if you wanted to add an external link sidebar entry using this file:
+# - section: "docs"
+#   chapter: "getting-started"
+#   name: "Container Installation"
+#   url: "https://docs.nextstrain.org/projects/cli/en/latest/installation/"

static-site/content/blog/2018-05-14-new-nextstrain-website.md

@@ -17,7 +17,7 @@ The only complicated aspect is deciding whether to serve auspice or Gatsby files
 
 **The static site:** can be found [here](https://github.com/nextstrain/static) and is build using [Gatsby](https://www.gatsbyjs.org/).
 This comprises the splash page and documentation (docs, about, blogs etc) all build from markdown files.
-[This page](/docs/static-content/introduction) explains the structure of the static page and shows how to add content – it's really easy ;).
+[This page](https://github.com/nextstrain/nextstrain.org/tree/master/static-site#nextstrain-static-site) explains the structure of the static page and shows how to add content – it's really easy ;).
 
 
 **Auspice:** is the visualisation app, build as a single page javascript application ([github](https://github.com/nextstrain/auspice)).

static-site/content/blog/2019-10-21-auspice-v2.md

@@ -2,6 +2,7 @@
 author: "James Hadfield"
 date: "2019-10-21"
 title: "Auspice v2 released"
+anchorText: "Auspice v2"
 ---
 
 ## What's New