sources: Reorganize from one long file into several shorter files

I found it was starting to get harder to find your way around and ignore
adjacent things that weren't relevant.

No functional code changes; only added lines which aren't identical
copies of removed lines are for require() path adjustments.

src/sources/community.js

@@ -0,0 +1,148 @@
+/* eslint no-use-before-define: ["error", {"functions": false, "classes": false}] */
+const {fetch} = require("../fetch");
+const queryString = require("query-string");
+const {NotFound} = require('http-errors');
+const utils = require("../utils");
+const {Source, Dataset, Narrative} = require("./models");
+
+class CommunitySource extends Source {
+  constructor(owner, repoName) {
+    super();
+
+    // The GitHub owner and repo names are required.
+    if (!owner) throw new Error(`Cannot construct a ${this.constructor.name} without an owner`);
+    if (!repoName) throw new Error(`Cannot construct a ${this.constructor.name} without a repoName`);
+
+    this.owner = owner;
+    [this.repoName, this.branch] = repoName.split(/@/, 2);
+    this.branchExplicitlyDefined = !!this.branch;
+
+    if (!this.repoName) throw new Error(`Cannot construct a ${this.constructor.name} without a repoName after splitting on /@/`);
+
+    this.defaultBranch = fetch(`https://api.github.com/repos/${this.owner}/${this.repoName}`)
+      .then((res) => res.json())
+      .then((data) => data.default_branch)
+      .catch(() => {
+        console.log(`Error interpreting the default branch of ${this.constructor.name} for ${this.owner}/${this.repoName}`);
+        return "master";
+      });
+    if (!this.branch) {
+      this.branch = this.defaultBranch;
+    }
+  }
+
+  static get _name() { return "community"; }
+  get repo() { return `${this.owner}/${this.repoName}`; }
+  async baseUrl() {
+    return `https://github.com/${this.repo}/raw/${await this.branch}/`;
+  }
+
+  async repoNameWithBranch() {
+    const branch = await this.branch;
+    const defaultBranch = await this.defaultBranch;
+    if (branch === defaultBranch && !this.branchExplicitlyDefined) {
+      return this.repoName;
+    }
+    return `${this.repoName}@${branch}`;
+  }
+
+  dataset(pathParts) {
+    return new CommunityDataset(this, pathParts);
+  }
+  narrative(pathParts) {
+    return new CommunityNarrative(this, pathParts);
+  }
+
+  async availableDatasets() {
+    const qs = queryString.stringify({ref: await this.branch});
+    const response = await fetch(`https://api.github.com/repos/${this.repo}/contents/auspice?${qs}`);
+
+    if (response.status === 404) throw new NotFound();
+    else if (response.status !== 200 && response.status !== 304) {
+      utils.warn(`Error fetching available datasets from GitHub for source ${this.name}`, await utils.responseDetails(response));
+      return [];
+    }
+
+    const filenames = (await response.json())
+      .filter((file) => file.type === "file")
+      // remove anything which doesn't start with the repo name, which is required of community datasets
+      .filter((file) => file.name.startsWith(this.repoName))
+      .map((file) => file.name);
+    const pathnames = utils.getDatasetsFromListOfFilenames(filenames)
+      // strip out the repo name from the start of the pathnames
+      // as CommunityDataset().baseParts will add this in
+      .map((pathname) => pathname.replace(`${this.repoName}/`, ""));
+    return pathnames;
+  }
+
+  async availableNarratives() {
+    const qs = queryString.stringify({ref: await this.branch});
+    const response = await fetch(`https://api.github.com/repos/${this.repo}/contents/narratives?${qs}`);
+
+    if (response.status !== 200 && response.status !== 304) {
+      if (response.status !== 404) {
+        // not found doesn't warrant an error print, it means there are no narratives for this repo
+        utils.warn(`Error fetching available narratives from GitHub for source ${this.name}`, await utils.responseDetails(response));
+      }
+      return [];
+    }
+
+    const files = await response.json();
+    return files
+      .filter((file) => file.type === "file")
+      .filter((file) => file.name !== "README.md")
+      .filter((file) => file.name.endsWith(".md"))
+      .filter((file) => file.name.startsWith(this.repoName))
+      .map((file) => file.name
+        .replace(this.repoName, "")
+        .replace(/^_/, "")
+        .replace(/[.]md$/, "")
+        .split("_")
+        .join("/"));
+  }
+  async getInfo() {
+    /* could attempt to fetch a certain file from the repository if we want to implement
+    this functionality in the future */
+    const branch = await this.branch;
+    return {
+      title: `${this.owner}'s "${this.repoName}" community builds`,
+      byline: `
+        Nextstrain community builds for GitHub → ${this.owner}/${this.repoName} (${branch} branch).
+        The available datasets and narratives in this repository are listed below.
+      `,
+      website: null,
+      showDatasets: true,
+      showNarratives: true,
+      /* avatar could be fetched here & sent in base64 or similar, or a link sent. The former (or similar) has the advantage
+      of private S3 buckets working, else the client will have to make (a) an authenticated request (too much work)
+      or (b) a subsequent request to nextstrain.org/charon (why not do it at once?) */
+      avatar: `https://github.com/${this.owner}.png?size=200`
+    };
+  }
+}
+
+class CommunityDataset extends Dataset {
+  get baseParts() {
+    // We require datasets are in the auspice/ directory and include the repo
+    // name in the file basename.
+    return [`auspice/${this.source.repoName}`, ...this.pathParts];
+  }
+  get isRequestValidWithoutDataset() {
+    if (!this.pathParts.length) {
+      return true;
+    }
+    return false;
+  }
+}
+
+class CommunityNarrative extends Narrative {
+  get baseParts() {
+    // We require narratives are in the narratives/ directory and include the
+    // repo name in the file basename.
+    return [`narratives/${this.source.repoName}`, ...this.pathParts];
+  }
+}
+
+module.exports = {
+  CommunitySource,
+};

src/sources/core.js

@@ -0,0 +1,71 @@
+const {fetch} = require("../fetch");
+const queryString = require("query-string");
+const {NotFound} = require('http-errors');
+const utils = require("../utils");
+const {Source} = require("./models");
+
+class CoreSource extends Source {
+  static get _name() { return "core"; }
+  async baseUrl() { return "http://data.nextstrain.org/"; }
+  get repo() { return "nextstrain/narratives"; }
+  get branch() { return "master"; }
+
+  async urlFor(path, method = 'GET') { // eslint-disable-line no-unused-vars
+    const baseUrl = path.endsWith(".md")
+      ? `https://raw.githubusercontent.com/${this.repo}/${await this.branch}/`
+      : await this.baseUrl();
+
+    const url = new URL(path, baseUrl);
+    return url.toString();
+  }
+
+  // The computation of these globals should move here.
+  secondTreeOptions(path) {
+    return (global.availableDatasets.secondTreeOptions[this.name] || {})[path] || [];
+  }
+
+  availableDatasets() {
+    return global.availableDatasets[this.name] || [];
+  }
+
+  async availableNarratives() {
+    const qs = queryString.stringify({ref: this.branch});
+    const response = await fetch(`https://api.github.com/repos/${this.repo}/contents?${qs}`);
+
+    if (response.status === 404) throw new NotFound();
+    else if (response.status !== 200 && response.status !== 304) {
+      utils.warn(`Error fetching available narratives from GitHub for source ${this.name}`, await utils.responseDetails(response));
+      return [];
+    }
+
+    const files = await response.json();
+    return files
+      .filter((file) => file.type === "file")
+      .filter((file) => file.name !== "README.md")
+      .filter((file) => file.name.endsWith(".md"))
+      .map((file) => file.name
+        .replace(/[.]md$/, "")
+        .split("_")
+        .join("/"));
+  }
+
+  async getInfo() {
+    return {
+      title: `Nextstrain ${this.name} datasets & narratives`,
+      showDatasets: true,
+      showNarratives: true,
+    };
+  }
+}
+
+class CoreStagingSource extends CoreSource {
+  static get _name() { return "staging"; }
+  async baseUrl() { return "http://staging.nextstrain.org/"; }
+  get repo() { return "nextstrain/narratives"; }
+  get branch() { return "staging"; }
+}
+
+module.exports = {
+  CoreSource,
+  CoreStagingSource,
+};

src/sources/fetch.js

@@ -0,0 +1,72 @@
+/* eslint no-use-before-define: ["error", {"functions": false, "classes": false}] */
+const {Source, Dataset, DatasetSubresource, Narrative, NarrativeSubresource} = require("./models");
+
+class UrlDefinedSource extends Source {
+  static get _name() { return "fetch"; }
+
+  constructor(authority) {
+    super();
+
+    if (!authority) throw new Error(`Cannot construct a ${this.constructor.name} without a URL authority`);
+
+    this.authority = authority;
+  }
+
+  async baseUrl() {
+    return `https://${this.authority}`;
+  }
+  dataset(pathParts) {
+    return new UrlDefinedDataset(this, pathParts);
+  }
+  narrative(pathParts) {
+    return new UrlDefinedNarrative(this, pathParts);
+  }
+
+  // available datasets & narratives are unknown when the dataset is specified by the URL
+  async availableDatasets() { return []; }
+  async availableNarratives() { return []; }
+  async getInfo() { return {}; }
+}
+
+class UrlDefinedDataset extends Dataset {
+  get baseName() {
+    return this.baseParts.join("/");
+  }
+  subresource(type) {
+    return new UrlDefinedDatasetSubresource(this, type);
+  }
+}
+
+class UrlDefinedDatasetSubresource extends DatasetSubresource {
+  get baseName() {
+    const type = this.type;
+    const baseName = this.resource.baseName;
+
+    if (type === "main") {
+      return baseName;
+    }
+
+    return baseName.endsWith(".json")
+      ? `${baseName.replace(/\.json$/, '')}_${type}.json`
+      : `${baseName}_${type}`;
+  }
+}
+
+class UrlDefinedNarrative extends Narrative {
+  get baseName() {
+    return this.baseParts.join("/");
+  }
+  subresource(type) {
+    return new UrlDefinedNarrativeSubresource(this, type);
+  }
+}
+
+class UrlDefinedNarrativeSubresource extends NarrativeSubresource {
+  get baseName() {
+    return this.resource.baseName;
+  }
+}
+
+module.exports = {
+  UrlDefinedSource,
+};